Tag: Bioconductor

Bioconductor – MCRestimate

DOI: 10.18129/B9.bioc.MCRestimate     Misclassification error estimation with cross-validation Bioconductor version: Release (3.6) This package includes a function for combining preprocessing and classification methods to calculate misclassification errors Author: Marc Johannes, Markus Ruschhaupt, Holger Froehlich, Ulrich Mansmann, Andreas Buness, Patrick Warnat, Wolfgang Huber, Axel Benner, Tim Beissbarth Maintainer: Marc Johannes…

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Bioconductor – genomation

DOI: 10.18129/B9.bioc.genomation     Summary, annotation and visualization of genomic data Bioconductor version: Release (3.6) A package for summary and annotation of genomic intervals. Users can visualize and quantify genomic intervals over pre-defined functional regions, such as promoters, exons, introns, etc. The genomic intervals represent regions with a defined chromosome…

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Bioconductor – BioNERO

DOI: 10.18129/B9.bioc.BioNERO     This package is for version 3.15 of Bioconductor; for the stable, up-to-date release version, see BioNERO. Biological Network Reconstruction Omnibus Bioconductor version: 3.15 BioNERO aims to integrate all aspects of biological network inference in a single package, including data preprocessing, exploratory analyses, network inference, and analyses…

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Bioconductor – Removed Packages

A list of packages removed from Bioconductor along with their last-available landing pages. Packages deprecated in Bioconductor 3.18 release (to be removed in 3.19) Software Packages: Experiment Data Packages: Packages removed with Bioconductor 3.18 release Software Packages: Experiment Data Packages: Packages removed with Bioconductor 3.17 release Software Packages: Experiment Data…

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Bioconductor Code: yarn

[![Travis-CI Build Status](https://travis-ci.org/jnpaulson/yarn.svg?branch=master)](https://travis-ci.org/QuackenbushLab/yarn) # YARN: Robust Multi-Tissue RNA-Seq Preprocessing and Normalization The goal of yarn is to expedite large RNA-seq analyses using a combination of previously developed tools. Yarn is meant to make it easier for the user to perform accurate comparison of conditions by leveraging many Bioconductor tools and…

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Bioconductor – mgu74cv2probe

DOI: 10.18129/B9.bioc.mgu74cv2probe     This package is for version 3.12 of Bioconductor; for the stable, up-to-date release version, see mgu74cv2probe. Probe sequence data for microarrays of type mgu74cv2 Bioconductor version: 3.12 This package was automatically created by package AnnotationForge version 1.11.21. The probe sequence data was obtained from http://www.affymetrix.com. The…

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Bioconductor – hu35ksubd.db

DOI: 10.18129/B9.bioc.hu35ksubd.db     This package is for version 3.12 of Bioconductor; for the stable, up-to-date release version, see hu35ksubd.db. Affymetrix Human Genome HU35K Set annotation data (chip hu35ksubd) Bioconductor version: 3.12 Affymetrix Human Genome HU35K Set annotation data (chip hu35ksubd) assembled using data from public repositories Author: Marc Carlson…

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Bioconductor – dcanr

DOI: 10.18129/B9.bioc.dcanr     This package is for version 3.12 of Bioconductor; for the stable, up-to-date release version, see dcanr. Differential co-expression/association network analysis Bioconductor version: 3.12 Methods and an evaluation framework for the inference of differential co-expression/association networks. Author: Dharmesh D. Bhuva [aut, cre] Maintainer: Dharmesh D. Bhuva <bhuva.d…

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Bioconductor – hgug4112a.db

DOI: 10.18129/B9.bioc.hgug4112a.db   Agilent “Human Genome, Whole” annotation data (chip hgug4112a) Bioconductor version: Release (3.18) Agilent “Human Genome, Whole” annotation data (chip hgug4112a) assembled using data from public repositories Author: Marc Carlson Maintainer: Bioconductor Package Maintainer <maintainer at bioconductor.org> Citation (from within R, enter citation(“hgug4112a.db”)): Installation To install this package,…

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Bioconductor – KinSwingR

DOI: 10.18129/B9.bioc.KinSwingR     This package is for version 3.8 of Bioconductor; for the stable, up-to-date release version, see KinSwingR. KinSwingR: network-based kinase activity prediction Bioconductor version: 3.8 KinSwingR integrates phosphosite data derived from mass-spectrometry data and kinase-substrate predictions to predict kinase activity. Several functions allow the user to build…

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Flow cytometry data analysis with R/Bioconductor course

News:Flow cytometry data analysis with R/Bioconductor course 0 Dear all, there are still a few seats available for our upcoming online course, “FLOW CYTOMETRY DATA ANALYSIS WITH R/BIOCONDUCTOR” (2nd edition) taking place from January 15th to January 18th, 2024. In this course, you will learn the fundamentals of flow cytometry…

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Notch signaling in thyrocytes is essential for adult thyroid function and mammalian homeostasis

Brent, G. A. Mechanisms of thyroid hormone action. J. Clin. Invest. 9, 3035–3043 (2012). Article  Google Scholar  Iwen, K. A., Oelkrug, R. & Brabant, G. Effects of thyroid hormones on thermogenesis and energy partitioning. J. Mol. Endocrinol. 60, R157–R170 (2018). Article  PubMed  CAS  Google Scholar  Biondi, B. & Wartofsky, L….

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Senior Scientist/Principal Scientist, Bioinformatics and Data Science, Cambridge, Massachusetts

Position Summary: Stealth NewCo is a discovery-stage biotechnology company leveraging insights in RNA biology to discover and develop new therapeutics for indications across multiple disease areas including oncology and neuromuscular disorders. We are seeking a talented Bioinformatics and Data Science Senior/Principal Scientist with experience analyzing multidimensional chemical, biological, and sequencing…

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Mapmygenome Jobs For Bioinformatics – Analyst Vacancy

–Must See– Mapmygenome Jobs For Bioinformatics – Analyst Vacancy Hot Job Opportunity: Bioinformatics Analyst at Mapmygenome™! Mapmygenome™ is a leading genomics company based in Hyderabad. We specialize in providing personalized healthcare solutions based on an individual’s genetic makeup. Our mission is to empower individuals to make informed choices about their…

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Bioconductor – PROMISE

DOI: 10.18129/B9.bioc.PROMISE     This package is for version 3.11 of Bioconductor; for the stable, up-to-date release version, see PROMISE. PRojection Onto the Most Interesting Statistical Evidence Bioconductor version: 3.11 A general tool to identify genomic features with a specific biologically interesting pattern of associations with multiple endpoint variables as…

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Use of data packages in containers

Use of data packages in containers 0 @893555ac Last seen 7 hours ago Germany For the Galaxy project we build quite a few containers that contain data packages (I hope I use the correct terms here) like bioconductor-org.Hs.eg.db. Often it’s many of such data packages which leads to large container…

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Single-cell RNA-seq workflow

In this tutorial we walk through a typical single-cell RNA-seq analysis using Bioconductor packages. We will try to cover data from different protocols, but some of the EDA/QC steps will be focused on the 10X Genomics Chromium protocol. We start from the output of the Cell Ranger preprocessing software. This…

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Bioconductor – chimeraviz

DOI: 10.18129/B9.bioc.chimeraviz     This package is for version 3.12 of Bioconductor; for the stable, up-to-date release version, see chimeraviz. Visualization tools for gene fusions Bioconductor version: 3.12 chimeraviz manages data from fusion gene finders and provides useful visualization tools. Author: Stian Lågstad [aut, cre], Sen Zhao [ctb], Andreas M….

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Bioconductor – RTN

DOI: 10.18129/B9.bioc.RTN     This package is for version 3.12 of Bioconductor; for the stable, up-to-date release version, see RTN. RTN: Reconstruction of Transcriptional regulatory Networks and analysis of regulons Bioconductor version: 3.12 A transcriptional regulatory network (TRN) consists of a collection of transcription factors (TFs) and the regulated target…

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Getting gene counts from transcript counts using R package ‘tximport’

Getting gene counts from transcript counts using R package ‘tximport’ 1 Hi everyone, I am working with RNA-seq data analysis. I want to convert transcript counts to gene counts. I have estimate counts of transcript using Kallisto and I want to use tximport R package to get counts for gene…

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Bioconductor – clusterProfiler

DOI: 10.18129/B9.bioc.clusterProfiler     This package is for version 3.12 of Bioconductor; for the stable, up-to-date release version, see clusterProfiler. statistical analysis and visualization of functional profiles for genes and gene clusters Bioconductor version: 3.12 This package implements methods to analyze and visualize functional profiles (GO and KEGG) of gene…

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Bioconductor T2T-CHM13

Comment: Reduce single cell experiment size to use as reference for annotation with Singl by elgomez • 0 Thank you, James! I ended up running seurat FindVariableFeatures with nfeatures = 10000 and then subsetting the object to just those varia… Comment: Help with model.matrix and creating the right contrast matrix…

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Bioconductor – airway

DOI: 10.18129/B9.bioc.airway     This package is for version 3.15 of Bioconductor; for the stable, up-to-date release version, see airway. RangedSummarizedExperiment for RNA-Seq in airway smooth muscle cells, by Himes et al PLoS One 2014 Bioconductor version: 3.15 This package provides a RangedSummarizedExperiment object of read counts in genes for…

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Bioconductor – ecoliasv2probe

DOI: 10.18129/B9.bioc.ecoliasv2probe     This package is for version 3.8 of Bioconductor; for the stable, up-to-date release version, see ecoliasv2probe. Probe sequence data for microarrays of type ecoliasv2 Bioconductor version: 3.8 This package was automatically created by package AnnotationForge version 1.11.21. The probe sequence data was obtained from http://www.affymetrix.com. The…

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Bioconductor – RProtoBufLib

DOI: 10.18129/B9.bioc.RProtoBufLib     This package is for version 3.7 of Bioconductor; for the stable, up-to-date release version, see RProtoBufLib. C++ headers and static libraries of Protocol buffers Bioconductor version: 3.7 This package provides the headers and static library of Protocol buffers 2.6.0 for other R packages to compile and…

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Bioconductor – hgu95av2.db

DOI: 10.18129/B9.bioc.hgu95av2.db   Affymetrix Affymetrix HG_U95Av2 Array annotation data (chip hgu95av2) Bioconductor version: Release (3.18) Affymetrix Affymetrix HG_U95Av2 Array annotation data (chip hgu95av2) assembled using data from public repositories Author: Marc Carlson Maintainer: Bioconductor Package Maintainer <maintainer at bioconductor.org> Citation (from within R, enter citation(“hgu95av2.db”)): Installation To install this package,…

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Bioconductor – QTLExperiment (development version)

DOI: 10.18129/B9.bioc.QTLExperiment   This is the development version of QTLExperiment; for the stable release version, see QTLExperiment. S4 classes for QTL summary statistics and metadata Bioconductor version: Development (3.19) QLTExperiment defines an S4 class for storing and manipulating summary statistics from QTL mapping experiments in one or more states. It…

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Bioconductor Code: phenomis

— editor_options: markdown: wrap: 72 — # **phenomis**: An R package for post-processing and univariate analysis [![Travis build status](https://travis-ci.org/SciDoPhenIA/phenomis.svg?branch=master)](https://travis-ci.org/odisce/phenomis) ## Description This package provides methods to perform the statistical analysis of phenomics datasets (e.g. in proteomics and metabolomics). These methods include the reading of datasets (as 3 table *dataMatrix*, *sampleMetadata*…

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Bioconductor GraphAndNetwork

Comment: flowCore >2.0 read.FCS results in $SPILLOVER error when reading certain FCS file by SamGG &utrif; 320 Hi. rbio2021 has no spillover, so no problem with current flowCore. As you identified it, the spillover matrix of rbio2023 has a header bu… Answer: Running DESeq on normalized data by James W….

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Drug repositioning using multiple gene expression profiles

Chuo University’s Professor Y-h. Taguchi places focus on drug repositioning using multiple gene expression profiles In my previous manuscripts (1-3), I introduced our studies of in silico drug repositioning using gene expression profiles. Nevertheless, in these studies, we could use the single gene expression profile to perform in silico drug…

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Stream [ACCESS] EBOOK EPUB KINDLE PDF Omic Association Studies with R and Bioconductor by Juan R. Gonz&aacu by juanailanaaiyanaxaa

published on 2023-12-12T21:06:52Z 💚 [PDF] FREE Omic Association Studies with R and Bioconductor by Juan R. González,Alejandro Cáceres Its work: [ACCESS] Omic Association Studies with R and Bioconductor by Juan R. González,Alejandro Cáceres EBOOK EPUB KINDLE PDF 📣 https://topstarsmedia.blogspot.gr/3X2aIXGuX1/1138340561 Omic Association Studies with R and Bioconductor by Juan R. González,Alejandro…

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Methylation Analysis Tutorial in R_part1

The code and approaches that I share here are those I am using to analyze TCGA methylation data. At the bottom of the page, you can find references used to make this tutorial. If you are coming from a computer background, please bear with a geneticist who tried to code…

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Transition of allele-specific DNA hydroxymethylation at regulatory loci is associated with phenotypic variation in monozygotic twins discordant for psychiatric disorders | BMC Medicine

Lichtenstein P, Yip BH, Bjork C, Pawitan Y, Cannon TD, Sullivan PF, Hultman CM. Common genetic determinants of schizophrenia and bipolar disorder in Swedish families: a population-based study. Lancet. 2009;373(9659):234–9. Article  PubMed  Google Scholar  Maurano MT, Humbert R, Rynes E, Thurman RE, Haugen E, Wang H, Reynolds AP, Sandstrom R,…

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Solved Currently, ENSEMBL GENE IDs with their versions

Currently, ENSEMBL GENE IDs with their versions represent each unique gene in each row. As an example, for ENSG00000000003.15, ENSG00000000003 represents the unique Ensembl gene ID and 15 represents the version. In biology, we are more familiar with the gene symbol, known as the HGNC SYMBOL. ENSG00000000003.15 Ensembl ID corresponds…

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Dispersal from the Qinghai-Tibet plateau by a high-altitude butterfly is associated with rapid expansion and reorganization of its genome

Zachos, J., Pagani, H., Sloan, L., Thomas, E. & Billups, K. Trends, rhythms, and aberrations in global climate 65 Ma to present. Science 292, 686–693 (2001). Article  ADS  CAS  PubMed  Google Scholar  Favre, A. et al. The role of the uplift of the Qinghai-Tibetan Plateau for the evolution of Tibetan…

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Bioconductor – Rgin

DOI: 10.18129/B9.bioc.Rgin     This package is for version 3.9 of Bioconductor; for the stable, up-to-date release version, see Rgin. gin in R Bioconductor version: 3.9 C++ implementation of SConES. Author: Hector Climente-Gonzalez [aut, cre], Dominik Gerhard Grimm [aut], Chloe-Agathe Azencott [aut] Maintainer: Hector Climente-Gonzalez <hector.climente at curie.fr> Citation (from…

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Bioconductor SeuratscRNA

Showing : SeuratscRNA • reset 1 day ago Bine &utrif; 20 1 result • Page 1 of 1 Recent … Replies Answer: Problems with FLOWAI by Alexander • 0 Hi. The length of the file path, or whether the files are local on the computer has nothing to do with…

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Bioconductor Code: plier

>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> The PLIER (Probe Logarithmic Error Intensity Estimate) method produces an improved signal by accounting for experimentally observed patterns in probe behavior and handling error at the appropriately at low and high signal values. Copyright (C) 2004 Affymetrix, Inc. and Paterson Institute for Cancer Research UK This program is free…

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Bioconductor Code: cytoMEM

# cytoMEM Marker Enrichment Modeling (MEM) is a tool designed to calculate enrichment scores. MEM generates human and machine readable labels that quantify the features enriched in a sample. The classic use of MEM is to identify multiple populations of cells and to compare each population to all of the…

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Bioconductor – pgca

DOI: 10.18129/B9.bioc.pgca     This package is for version 3.12 of Bioconductor; for the stable, up-to-date release version, see pgca. PGCA: An Algorithm to Link Protein Groups Created from MS/MS Data Bioconductor version: 3.12 Protein Group Code Algorithm (PGCA) is a computationally inexpensive algorithm to merge protein summaries from multiple…

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Bioconductor – IFAA (development version)

DOI: 10.18129/B9.bioc.IFAA   This is the development version of IFAA; for the stable release version, see IFAA. Robust Inference for Absolute Abundance in Microbiome Analysis Bioconductor version: Development (3.19) This package offers a robust approach to make inference on the association of covariates with the absolute abundance (AA) of microbiome…

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Bioconductor – pgxRpi (development version)

DOI: 10.18129/B9.bioc.pgxRpi   This is the development version of pgxRpi; to use it, please install the devel version of Bioconductor. R wrapper for Progenetix Bioconductor version: Development (3.19) The package is an R wrapper for Progenetix REST API built upon the Beacon v2 protocol. Its purpose is to provide a…

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Bioconductor – bcellViper (development version)

DOI: 10.18129/B9.bioc.bcellViper   This is the development version of bcellViper; for the stable release version, see bcellViper. Human B-cell transcriptional interactome and normal human B-cell expression data Bioconductor version: Development (3.19) This package provides a human B-cell context-specific transcriptional regulatory network and a human normal B-cells dataset for the examples…

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Bioconductor Code: CelliD

# CelliD v0.99 R package for gene signature extraction and cell identity recognition at individual cell level from single-cell RNA-seq. ![logo](https://github.com/RausellLab/CelliD/blob/gh-pages/tools/sticker.png?raw=true) —————————————- Welcome to the official Github repository of the **CelliD** software presented in the Article [Gene signature extraction and cell identity recognition at the single-cell level with Cell-ID, Nature…

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Bioconductor – BSgenome.Tguttata.UCSC.taeGut1

DOI: 10.18129/B9.bioc.BSgenome.Tguttata.UCSC.taeGut1     This package is for version 3.14 of Bioconductor; for the stable, up-to-date release version, see BSgenome.Tguttata.UCSC.taeGut1. Full genome sequences for Taeniopygia guttata (UCSC version taeGut1) Bioconductor version: 3.14 Full genome sequences for Taeniopygia guttata (Zebra finch) as provided by UCSC (taeGut1, Jul. 2008) and stored in…

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Course. – Gene Set Enrichment Analysis in R/Bioconductor

News:Course. – Gene Set Enrichment Analysis in R/Bioconductor – ONLINE, 22-25 January 0 Dear all, there are still 5 seats for the next edition of the online course on “Gene Set Enrichment Analysis in R/Bioconductor” taking place from January 22nd to January 25th, 2024. This course will cover popular GSEA…

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Bioconductor Code: SigCheck

 About browsing: devel Branches RELEASE_3_0 RELEASE_3_1 RELEASE_3_10 RELEASE_3_11 RELEASE_3_12 RELEASE_3_13 RELEASE_3_14 RELEASE_3_15 RELEASE_3_16 RELEASE_3_17 RELEASE_3_18 RELEASE_3_2 RELEASE_3_3 RELEASE_3_4 RELEASE_3_5 RELEASE_3_6 RELEASE_3_7 RELEASE_3_8 RELEASE_3_9 devel Files Commits Stats Network Graph SigCheck Clone ZIP TAR × SSH HTTPS Name Mode Size R 040000 data 040000 inst 040000 man 040000 vignettes 040000 DESCRIPTION…

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Bioconductor – hu35ksubc.db

DOI: 10.18129/B9.bioc.hu35ksubc.db     This package is for version 3.11 of Bioconductor; for the stable, up-to-date release version, see hu35ksubc.db. Affymetrix Human Genome HU35K Set annotation data (chip hu35ksubc) Bioconductor version: 3.11 Affymetrix Human Genome HU35K Set annotation data (chip hu35ksubc) assembled using data from public repositories Author: Marc Carlson…

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Sr. Scientist of Computational Biology/Bioinformatics at Flagship Pioneering, Inc. – Cambridge, MA USA

Company Summary: Each day, the lives of more than 2 billion people across the globe are impacted by chronic diseases. Moreover, the economic burden on society of treating chronic disease is spinning out of control. Today, this dire situation appears unlikely to change as >95% of global healthcare costs are…

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bronchialIL13

bronchialIL13 time course experiment involving il13 derived from CNMC (pepr.cnmcresearch.org) http://pepr.cnmcresearch.org/browse.do?action=list_prj_exp&projectId=95 Human Bronchial Cell line A549 Author Vince Carey Maintainer Vince Carey To install this package, start R and enter: source(“http://bioconductor.org/biocLite.R”) biocLite(“bronchialIL13”) Vignettes (Documentation) Package Downloads Details Read more here: Source link

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Software for Spatial Transcriptomic data [NanoString; Visium]?

Software for Spatial Transcriptomic data [NanoString; Visium]? 0 Hello Biostars, I was writing to ask if any of you have experience with data generated using either Nanostring GeoMx or 10X Visium. Our group has Nanostring data in hand and will be generating 10X Visium data soon-ish. So, most immediately we…

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Bioconductor – DropletUtils

DOI: 10.18129/B9.bioc.DropletUtils     This package is for version 3.15 of Bioconductor; for the stable, up-to-date release version, see DropletUtils. Utilities for Handling Single-Cell Droplet Data Bioconductor version: 3.15 Provides a number of utility functions for handling single-cell (RNA-seq) data from droplet technologies such as 10X Genomics. This includes data…

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Bioconductor – octad (development version)

DOI: 10.18129/B9.bioc.octad   This is the development version of octad; for the stable release version, see octad. Open Cancer TherApeutic Discovery (OCTAD) Bioconductor version: Development (3.19) OCTAD provides a platform for virtually screening compounds targeting precise cancer patient groups. The essential idea is to identify drugs that reverse the gene…

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[PDF] tRanslatome: an R/Bioconductor package to portray translational control

@article{Tebaldi2013tRanslatomeAR, title={tRanslatome: an R/Bioconductor package to portray translational control}, author={Toma Tebaldi and Erik Dassi and Galena Kostoska and Gabriella Viero and Alessandro Quattrone}, journal={Bioinformatics}, year={2013}, volume={30}, pages={289 – 291}, url={https://api.semanticscholar.org/CorpusID:2959187} } Summary: High-throughput technologies have led to an explosion of genomic data available for automated analysis. The consequent possibility to…

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Identification and validation of key miRNAs for colon cancer

Introduction With nearly 2 million new cases and 1 million deaths worldwide in 2020, colorectal cancer is the third-most common cancer and the second leading cause of cancer-related deaths.1 According to data from the US Surveillance, Epidemiology and End Results program and the National Program of Cancer Registries program, the…

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Bioconductor – BSgenome.Rnorvegicus.UCSC.rn7 (development version)

DOI: 10.18129/B9.bioc.BSgenome.Rnorvegicus.UCSC.rn7   This is the development version of BSgenome.Rnorvegicus.UCSC.rn7; for the stable release version, see BSgenome.Rnorvegicus.UCSC.rn7. Full genome sequences for Rattus norvegicus (UCSC genome rn7) Bioconductor version: Development (3.19) Full genome sequences for Rattus norvegicus (Rat) as provided by UCSC (genome rn7) and stored in Biostrings objects. Author: The…

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hgu133plus2.db

hgu133plus2.db Affymetrix Human Genome U133 Plus 2.0 Array annotation data (chip hgu133plus2) Affymetrix Human Genome U133 Plus 2.0 Array annotation data (chip hgu133plus2) assembled using data from public repositories Author Marc Carlson, Seth Falcon, Herve Pages, Nianhua Li Maintainer Biocore Data Team To install this package, start R and enter:…

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contrast file in DESeq2 bioconductor

contrast file in DESeq2 bioconductor 1 Hi everyone, I have 3 time points and want to do deseq2 for comparing these 3 time points: is it correct to build my contrast file like below? results(dds, contrast = c(“timepoints”, “TS”,”EOT”, “FU”)) I can also take TS (Therapy start) as control and…

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Bioconductor – mAPKLData (development version)

DOI: 10.18129/B9.bioc.mAPKLData   This is the development version of mAPKLData; for the stable release version, see mAPKLData. Gene expression data for testing of the package mAPKL. Bioconductor version: Development (3.19) Gene expression data from a breast cancer study published by Turashvili et al. in 2007, provided as an eSet. Author:…

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Bioconductor Code: daMA

 About browsing: devel Branches RELEASE_1_4 RELEASE_1_5 RELEASE_1_6 RELEASE_1_7 RELEASE_1_8 RELEASE_1_9 RELEASE_2_0 RELEASE_2_1 RELEASE_2_10 RELEASE_2_11 RELEASE_2_12 RELEASE_2_13 RELEASE_2_14 RELEASE_2_2 RELEASE_2_3 RELEASE_2_4 RELEASE_2_5 RELEASE_2_6 RELEASE_2_7 RELEASE_2_8 RELEASE_2_9 RELEASE_3_0 RELEASE_3_1 RELEASE_3_10 RELEASE_3_11 RELEASE_3_12 RELEASE_3_13 RELEASE_3_14 RELEASE_3_15 RELEASE_3_16 RELEASE_3_17 RELEASE_3_18 RELEASE_3_2 RELEASE_3_3 RELEASE_3_4 RELEASE_3_5 RELEASE_3_6 RELEASE_3_7 RELEASE_3_8 RELEASE_3_9 devel Files Commits Stats Network Graph…

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Bioconductor – hugene11sttranscriptcluster.db

DOI: 10.18129/B9.bioc.hugene11sttranscriptcluster.db     This package is for version 3.10 of Bioconductor; for the stable, up-to-date release version, see hugene11sttranscriptcluster.db. Affymetrix hugene11 annotation data (chip hugene11sttranscriptcluster) Bioconductor version: 3.10 Affymetrix hugene11 annotation data (chip hugene11sttranscriptcluster) assembled using data from public repositories Author: James W. MacDonald Maintainer: Biocore Package Maintainer <maintainer…

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Bioconductor – hmyriB36

DOI: 10.18129/B9.bioc.hmyriB36     This package is deprecated. It will probably be removed from Bioconductor. Please refer to the package end-of-life guidelines for more information. This package is for version 3.13 of Bioconductor. This package has been removed from Bioconductor. For the last stable, up-to-date release version, see hmyriB36. YRI…

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Bioconductor Code: metagenomeSeq

metagenomeSeq ============= Statistical analysis for sparse high-throughput sequencing [![Travis-CI Build Status](https://travis-ci.org/HCBravoLab/metagenomeSeq.svg?branch=master)](https://travis-ci.org/HCBravoLab/metagenomeSeq) <a href=”http://www.bioconductor.org/packages/devel/bioc/html/metagenomeSeq.html#since”><img border=”0″ src=”http://www.bioconductor.org/shields/years-in-bioc/metagenomeSeq.svg” title=”How long since the package was first in a released Bioconductor version (or is it in devel only).”></a> <a href=”http://bioconductor.org/packages/stats/bioc/metagenomeSeq.html”><img border=”0″ src=”http://www.bioconductor.org/shields/downloads/metagenomeSeq.svg” title=”Percentile (top 5/20/50% or ‘available’) of downloads over last 6 full months. Comparison…

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Bioconductor – epivizrChart

DOI: 10.18129/B9.bioc.epivizrChart     This package is for version 3.14 of Bioconductor; for the stable, up-to-date release version, see epivizrChart. R interface to epiviz web components Bioconductor version: 3.14 This package provides an API for interactive visualization of genomic data using epiviz web components. Objects in R/BioConductor can be used…

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Bioconductor – hapmap500ksty

DOI: 10.18129/B9.bioc.hapmap500ksty   Sample data – Hapmap 500K STY Affymetrix Bioconductor version: Release (3.18) Sample dataset obtained from http://www.hapmap.org Author: Hapmap Consortium Maintainer: Benilton Carvalho <Benilton.Carvalho at cancer.org.uk> Citation (from within R, enter citation(“hapmap500ksty”)): Installation To install this package, start R (version “4.3”) and enter: if (!require(“BiocManager”, quietly = TRUE))…

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Bioconductor – semisup

DOI: 10.18129/B9.bioc.semisup   This package is for version 3.16 of Bioconductor; for the stable, up-to-date release version, see semisup. Semi-Supervised Mixture Model Bioconductor version: 3.16 Implements a parametric semi-supervised mixture model. The permutation test detects markers with main or interactive effects, without distinguishing them. Possible applications include genome-wide association analysis…

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Why is DMRcate not available for Bioconductor version 3.18?

Why is DMRcate not available for Bioconductor version 3.18? 0 @daniel-e-weeks-10677 Last seen 22 hours ago Pittsburgh, Pennsylvania, United States… According to the Bioconductor web page for DMRcate, it looks like it is available for Bioconductor version 3.18 but this installation fails: > BiocManager::install(“DMRcate”) Bioconductor version 3.18 (BiocManager 1.30.22), R…

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RStudio For Quantitative Finance

Introduction to RStudio R is widely used in quantitative finance due to its extensive statistical capabilities, data manipulation tools, and its active community that develops and maintains specialized packages for finance. It offers a wide range of functionalities that enable professionals in the finance industry to analyze data, build models,…

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Bioconductor – SIFT.Hsapiens.dbSNP132

DOI: 10.18129/B9.bioc.SIFT.Hsapiens.dbSNP132   This package is for version 3.16 of Bioconductor; for the stable, up-to-date release version, see SIFT.Hsapiens.dbSNP132. SIFT Predictions for Homo sapiens dbSNP build 132 Bioconductor version: 3.16 Database of SIFT predictions for Homo sapiens dbSNP build 132 Author: Valerie Obenchain Maintainer: Valerie Obenchain <vobencha at fhcrc.org> Citation…

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Which program, tool, or strategy do you use to visualize genomic rearrangements?

Which program, tool, or strategy do you use to visualize genomic rearrangements? 5 Which program, tool, or strategy do you use to visualize genomic rearrangements? In relation to my master thesis I’m working on tools to visualize fusion genes. In that regard I’m interested in any and all strategies and…

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Salpa genome and developmental transcriptome analyses reveal molecular flexibility enabling reproductive success in a rapidly changing environment

Loeb, V. et al. Effects of sea-ice extent and krill or salp dominance on the Antarctic food web. Nature 387, 897–900 (1997). Article  ADS  CAS  Google Scholar  Atkinson, A., Siegel, V., Pakhomov, E. & Rothery, P. Long-term decline in krill stock and increase in salps within the Southern Ocean. Nature…

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Bioconductor Code: distinct

# distinct: a method for differential analyses via hierarchical permutation tests <img src=”inst/extdata/distinct.png” width=”200″ align=”right”/> `distinct` is a statistical method to perform differential testing between two or more groups of distributions; differential testing is performed via non-parametric permutation tests on the cumulative distribution functions (cdfs) of each sample. `distinct` is…

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Bioconductor – crisprBase

DOI: 10.18129/B9.bioc.crisprBase   This package is for version 3.16 of Bioconductor; for the stable, up-to-date release version, see crisprBase. Base functions and classes for CRISPR gRNA design Bioconductor version: 3.16 Provides S4 classes for general nucleases, CRISPR nucleases, CRISPR nickases, and base editors.Several CRISPR-specific genome arithmetic functions are implemented to…

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Bioconductor – maqcExpression4plex

DOI: 10.18129/B9.bioc.maqcExpression4plex   Sample Expression Data – MAQC / HG18 – NimbleGen Bioconductor version: Release (3.18) Data from human (HG18) 4plex NimbleGen array. It has 24k genes with 3 60mer probes per gene. Author: NimbleGen Systems Maintainer: Benilton Carvalho <Benilton.Carvalho at cancer.org.uk> Citation (from within R, enter citation(“maqcExpression4plex”)): Installation To…

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Longitudinal detection of circulating tumor DNA

Analysis of Roche KAPA Target Enrichment kit experimental data obtained on an Illumina sequencing system is most frequently performed using a variety of publicly available, open-source analysis tools. The typical variant calling analysis workflow consists of sequencing read quality assessment, read filtering, mapping against the reference genome, duplicate removal, coverage…

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Bioinformatics Jobs and Scope in India – Top 10 Jobs in Bioinformatics

Bioinformatics develops as a region of limitless possibility in the  science and technology, where biology converges with computing capability. Consider a future in which every strand of DNA contains the key to revolutionary discoveries and individualized therapy. Welcome to the dynamic world of Bioinformatics, a discipline that bridges conventional divides…

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Bioconductor – KEGGdzPathwaysGEO

DOI: 10.18129/B9.bioc.KEGGdzPathwaysGEO   KEGG Disease Datasets from GEO Bioconductor version: Release (3.18) This is a collection of 24 data sets for which the phenotype is a disease with a corresponding pathway in the KEGG database.This collection of datasets were used as gold standard in comparing gene set analysis methods by…

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Bioconductor – ind1KG

    This package is for version 2.13 of Bioconductor; for the stable, up-to-date release version, see ind1KG. Data from 1000 Genomes, NA19240 (female) chr6 excerpt Bioconductor version: 2.13 Elements of samtools/bioc workflow for dealing with personal sequence focusing on identification and interpretation of rare variants Author: VJ Carey <stvjc…

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DEseq2 input

DEseq2 input 1 Hello Guys, @Michael Love I have a transcriptomics dataset and did rnaseq/nf-core pipeline by salmon-star. my output of the salmon-star folder is as follows: salmon.merged.gene_counts.tsv salmon.merged.gene_counts_length_scaled.tsv salmon.merged.gene_counts_scaled.tsv salmon.merged.gene_lengths.tsv salmon.merged.gene_tpm.tsv salmon.merged.transcript_counts.tsv salmon.merged.transcript_lengths.tsv salmon.merged.transcript_tpm.tsv tx2gene.tsv my question is: which one of these files should be an input for Deseq2…

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Raising money to package RStudio for the Nix package manager for macOS platforms – RStudio IDE

Dear community I am doing a Gofundme to raise the money required to package Rstudio for macOS platforms for the Nix package manager. Nix is a package manager that can be installed on Windows (through WSL2), Linux and macOS. If you’ve been using package managers on macOS, you might be…

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Bioconductor – nem

Nested Effects Models to reconstruct phenotypic hierarchies Bioconductor version: 2.5 The package ‘nem’ allows to reconstruct features of pathways from the nested structure of perturbation effects. It takes as input (1.) a set of pathway components, which were perturbed, and (2.) high-dimensional phenotypic readout of these perturbations (e.g. gene expression…

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Bioconductor Code: SNPRelate

SNPRelate: Parallel computing toolset for relatedness and principal component analysis of SNP data ==== ![GPLv3](http://www.gnu.org/graphics/gplv3-88×31.png) [GNU General Public License, GPLv3](http://www.gnu.org/copyleft/gpl.html) [![Availability](http://www.bioconductor.org/shields/availability/release/SNPRelate.svg)](http://www.bioconductor.org/packages/release/bioc/html/SNPRelate.html) [![Years-in-BioC](http://www.bioconductor.org/shields/years-in-bioc/SNPRelate.svg)](http://www.bioconductor.org/packages/release/bioc/html/SNPRelate.html) [![R](https://github.com/zhengxwen/SNPRelate/actions/workflows/r.yml/badge.svg)](https://github.com/zhengxwen/SNPRelate/actions/workflows/r.yml) ## Features Genome-wide association studies are widely used to investigate the genetic basis of diseases and traits, but they pose many computational challenges. We developed SNPRelate (R…

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Tools for Efficient Retrieval from GEO and SRA Databases | by Denis Odinokov, MBBS, MSc, PMP | Nov, 2023

Image by Gerd Altmann from Pixabay For downloading data and standardized metadata from GEO (Gene Expression Omnibus) and SRA (Sequence Read Archive), several bioinformatics and command-line tools and scripts are available, primarily hosted on GitHub. ARA: An automated pipeline developed for better sampling of NCBI SRA database records, allowing full…

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Bioconductor – gDNAx

DOI: 10.18129/B9.bioc.gDNAx   Diagnostics for assessing genomic DNA contamination in RNA-seq data Bioconductor version: Release (3.18) Provides diagnostics for assessing genomic DNA contamination in RNA-seq data, as well as plots representing these diagnostics. Moreover, the package can be used to get an insight into the strand library protocol used and,…

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Bioconductor – RdbiPgSQL

PostgreSQL access Bioconductor version: 2.5 Provides methods for accessing data stored in PostgreSQL tables. Code written by Timothy H. Keitt and modified by Jianhua Zhang Author: Timothy H. Keitt <thk at users.sourceforge.net> Maintainer: Jianhua Zhang <jzhang at jimmy.harvard.edu> To install this package, start R and enter: source(“http://bioconductor.org/biocLite.R”) biocLite(“RdbiPgSQL”) To cite…

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Bioconductor – limma

Linear Models for Microarray Data Bioconductor version: 2.5 Data analysis, linear models and differential expression for microarray data. Author: Gordon Smyth with contributions from Matthew Ritchie, Jeremy Silver, James Wettenhall, Natalie Thorne, Mette Langaas, Egil Ferkingstad, Marcus Davy, Francois Pepin, Dongseok Choi, Di Wu, Alicia Oshlack, Carolyn de Graaf, Yifang…

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Bioconductor – RankProd

Rank Product method for identifying differentially expressed genes with application in meta-analysis Bioconductor version: 2.5 Non-paramteric method for identifying differentially expressed (up- or down- regulated )genes based on the estimated percentage of false predictions (pfp).The method can combine data sets from different origins (meta-analysis)to increase the power of the identification….

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Subgenome dominance shapes novel gene evolution in the decaploid pitcher plant Nepenthes gracilis

Soltis, D. E. et al. Polyploidy and angiosperm diversification. Am. J. Bot. 96, 336–348 (2009). Article  PubMed  Google Scholar  Van de Peer, Y., Mizrachi, E. & Marchal, K. The evolutionary significance of polyploidy. Nat. Rev. Genet. 18, 411–424 (2017). Article  PubMed  Google Scholar  Amborella Genome Project et al. The Amborella…

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Bioconductor – PWMEnrich.Hsapiens.background

DOI: 10.18129/B9.bioc.PWMEnrich.Hsapiens.background     This package is for version 3.12 of Bioconductor; for the stable, up-to-date release version, see PWMEnrich.Hsapiens.background. H. sapiens background for PWMEnrich Bioconductor version: 3.12 PWMEnrich pre-compiled background objects for H. sapiens (human) and MotifDb H. sapiens motifs. Author: Robert Stojnic Maintainer: Diego Diez <diego10ruiz at gmail.com>…

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Diferences between TCGAbiolinks and cBioportal

Hi, Im exploring and integrating the LUAD TGCA transcriptomic and genomic data. Im trying to do so both with TCGAbiolinks in R and cBioportal. With TCGAbiolinks I acces the data this way (https://bioconductor.org/packages/devel/bioc/vignettes/TCGAbiolinks/inst/doc/analysis.html#TCGAvisualize:_Visualize_results_from_analysis_functions_with_TCGA%E2%80%99s_data) query <- GDCquery(#legacy = T, project = “TCGA-LUAD”, data.category = “Transcriptome Profiling”, data.type = “Gene Expression Quantification”,…

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A single pseudouridine on rRNA regulates ribosome structure and function in the mammalian parasite Trypanosoma brucei

Cell growth and transfections Procyclic form (PCF) T. brucei, strain 29-1354, which carries integrated genes for the T7 polymerase and the tetracycline repressor, was grown in SDM-79 medium supplemented with 10% fetal calf serum, in the presence of 50 μg/ml hygromycin. Cells were grown in the presence of 15 μg/ml G418 for…

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ChAMP can’t be found in Bioc3.18?

ChAMP can’t be found in Bioc3.18? 1 @8df9ba1f Last seen 6 hours ago Ireland Hi I am on Debian 12 (stable) and just installed R-4.3.2 and Bioconductor v3.18 successfully and then installed alot of my favourite Bioconductor packages. However with ChAMP, the DNA methylation package, it said it couldn’t be…

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Bioconductor – ppiData

DOI: 10.18129/B9.bioc.ppiData     This package is for version 3.9 of Bioconductor; for the stable, up-to-date release version, see ppiData. A package that contains the bait to prey directed graphs for protein-protein interactions. Bioconductor version: 3.9 This package contains the directed graphs for protein interaction data as derived from Y2H…

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Bioconductor – ptairMS

DOI: 10.18129/B9.bioc.ptairMS     Pre-processing PTR-TOF-MS Data Bioconductor version: Release (3.13) This package implements a suite of methods to preprocess data from PTR-TOF-MS instruments (HDF5 format) and generates the ‘sample by features’ table of peak intensities in addition to the sample and feature metadata (as a single ExpressionSet object for…

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Installation of DESeq2 package while utilizing free Posit cloud – General

Help! I’m trying to install DEseq2 to perform differential gene expression analysis R Studio. I’m using the free R Studio on Posit Cloud. R Sudio version is 4.3.2, BiocManager is 3.1.8. This is my issue with the error: library(BiocManager)Bioconductor version 3.18 (BiocManager 1.30.22), R 4.3.2 (2023-10-31)BiocManager::install(“DESeq2”)‘getOption(“repos”)’ replaces Bioconductor standard repositories,…

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DESeq2 installation failures

DESeq2 installation failures 0 Help! I’m trying to install DEseq2 to perform differential gene expression analysis R Studio. I’m using the free R Studio on Posit Cloud. R Sudio version is 4.3.2, BiocManager is 3.1.8. This is my issue with the error: library(BiocManager) Bioconductor version 3.18 (BiocManager 1.30.22), R 4.3.2…

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R bioc_install_repos — EndMemo

R bioc_install_repos bioc_version() returns the Bioconductor version for the current or the specified R version. bioc_install_repos is located in package remotes. Please install and load package remotes before use. bioc_version(r_ver = getRversion()) bioc_install_repos(r_ver = getRversion(), bioc_ver = bioc_version(r_ver)) r_ver R version to use. For bioc_install_repos() it is ignored if bioc_ver…

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Calculation of ChIP-seq normalization factors with non-conventional spike-in assumptions

Calculation of ChIP-seq normalization factors with non-conventional spike-in assumptions 0 I have an experimental setup where there are known global shifts in levels of our histone mark of interest due to a histone mutation. We include spike-in chromatin in each sample, but we know that the spikein levels are not…

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Diffbind low p-value but high FDR

Diffbind low p-value but high FDR 0 I guess my issue is related to this post https://support.bioconductor.org/p/85487/#85490. Here is the dba.report(DBA,th=1, bCounts=TRUE) results. One of the peaks clearly shows a significant difference in IGV (And we also expected it to be changed) and has a small p.vaule but the FDR…

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Bioinformatics Scientist, Solid Tumor DNA Oncology

Passionate about precision medicine and advancing the healthcare industry? Recent advancements in underlying technology have finally made it possible for AI to impact clinical care in a meaningful way. Tempus’ proprietary platform connects an entire ecosystem of real-world evidence to deliver real-time, actionable insights to physicians, providing critical information about…

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