Tag: GPL

Bioconductor – RDAVIDWebService

DOI: 10.18129/B9.bioc.RDAVIDWebService     This package is for version 3.12 of Bioconductor; for the stable, up-to-date release version, see RDAVIDWebService. An R Package for retrieving data from DAVID into R objects using Web Services API. Bioconductor version: 3.12 Tools for retrieving data from the Database for Annotation, Visualization and Integrated…

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Bioconductor – bnem (development version)

DOI: 10.18129/B9.bioc.bnem     This is the development version of bnem; for the stable release version, see bnem. Training of logical models from indirect measurements of perturbation experiments Bioconductor version: Development (3.15) bnem combines the use of indirect measurements of Nested Effects Models (package mnem) with the Boolean networks of…

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Bioconductor – ChIPQC

    This package is for version 3.1 of Bioconductor; for the stable, up-to-date release version, see ChIPQC. Quality metrics for ChIPseq data Bioconductor version: 3.1 Quality metrics for ChIPseq data Author: Tom Carroll, Wei Liu, Ines de Santiago, Rory Stark Maintainer: Tom Carroll <tc.infomatics at gmail.com>, Rory Stark <rory.stark…

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About QUAST

About Short intro Further reading How to cite Brief project history Authors Funding License and Terms of use Short intro QUAST evaluates genome assemblies by computing various metrics, including N50, length for which the collection of all contigs of that length or longer covers at least 50% of assembly length…

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Bioconductor – monaLisa

DOI: 10.18129/B9.bioc.monaLisa     Binned Motif Enrichment Analysis and Visualization Bioconductor version: Release (3.14) Useful functions to work with sequence motifs in the analysis of genomics data. These include methods to annotate genomic regions or sequences with predicted motif hits and to identify motifs that drive observed changes in accessibility…

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Bioconductor – ProteoDisco

DOI: 10.18129/B9.bioc.ProteoDisco     Generation of customized protein variant databases from genomic variants, splice-junctions and manual sequences Bioconductor version: Release (3.14) ProteoDisco is an R package to facilitate proteogenomics studies. It houses functions to create customized (mutant) protein databases based on user-submitted genomic variants, splice-junctions, fusion genes and manual transcript…

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Can you use scikit multilearn with scikit-learn?

You can use scikit-learn’s base classifiers as scikit-multilearn’s classifiers. In addition, the two packages follow a similar API. In most cases you will want to follow the requirements defined in the requirements/*.txt files in the package. This will install the latest release from the Python package index. If you Next,…

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Bioconductor – Rariant

    This package is for version 3.0 of Bioconductor; for the stable, up-to-date release version, see Rariant. Identification and Assessment of Single Nucleotide Variants through Shifts in Non-Consensus Base Call Frequencies Bioconductor version: 3.0 The ‘Rariant’ package identifies single nucleotide variants from sequencing data based on the difference of…

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CRAN – Package ggmatplot

CRAN – Package ggmatplot ggmatplot: Plot Columns of Two Matrices Against Each Other Using ‘ggplot2’ A quick and easy way of plotting the columns of two matrices or data frames against each other using ‘ggplot2’. Although ‘ggmatplot’ doesn’t provide the same flexibility as ‘ggplot2’, it can be used as a…

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Bioconductor – csaw

    This package is for version 3.2 of Bioconductor; for the stable, up-to-date release version, see csaw. ChIP-seq analysis with windows Bioconductor version: 3.2 Detection of differentially bound regions in ChIP-seq data with sliding windows, with methods for normalization and proper FDR control. Author: Aaron Lun <alun at wehi.edu.au>,…

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Bioconductor – pageRank

DOI: 10.18129/B9.bioc.pageRank     This package is for version 3.12 of Bioconductor; for the stable, up-to-date release version, see pageRank. Temporal and Multiplex PageRank for Gene Regulatory Network Analysis Bioconductor version: 3.12 Implemented temporal PageRank analysis as defined by Rozenshtein and Gionis. Implemented multiplex PageRank as defined by Halu et…

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Bioconductor – CAMERA

DOI: 10.18129/B9.bioc.CAMERA     This package is for version 3.12 of Bioconductor; for the stable, up-to-date release version, see CAMERA. Collection of annotation related methods for mass spectrometry data Bioconductor version: 3.12 Annotation of peaklists generated by xcms, rule based annotation of isotopes and adducts, isotope validation, EIC correlation based…

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[v2,01/12] iio:dac:ad5755: Switch to generic firmware properties and drop pdata

@@ -13,10 +13,9 @@ #include <linux/slab.h> #include <linux/sysfs.h> #include <linux/delay.h> -#include <linux/of.h> +#include <linux/property.h> #include <linux/iio/iio.h> #include <linux/iio/sysfs.h> -#include <linux/platform_data/ad5755.h> #define AD5755_NUM_CHANNELS 4 @@ -63,6 +62,101 @@ #define AD5755_SLEW_RATE_SHIFT 3 #define AD5755_SLEW_ENABLE BIT(12) +enum ad5755_mode { + AD5755_MODE_VOLTAGE_0V_5V = 0, + AD5755_MODE_VOLTAGE_0V_10V = 1, + AD5755_MODE_VOLTAGE_PLUSMINUS_5V = 2, + AD5755_MODE_VOLTAGE_PLUSMINUS_10V…

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Bioconductor – airpart

DOI: 10.18129/B9.bioc.airpart     This package is for version 3.13 of Bioconductor; for the stable, up-to-date release version, see airpart. Differential cell-type-specific allelic imbalance Bioconductor version: 3.13 Airpart identifies sets of genes displaying differential cell-type-specific allelic imbalance across cell types or states, utilizing single-cell allelic counts. It makes use of…

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Bioconductor – TFBSTools

    This package is for version 3.3 of Bioconductor; for the stable, up-to-date release version, see TFBSTools. Software Package for Transcription Factor Binding Site (TFBS) Analysis Bioconductor version: 3.3 TFBSTools is a package for the analysis and manipulation of transcription factor binding sites. It includes matrices conversion between Position…

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Bioconductor – GenVisR

DOI: 10.18129/B9.bioc.GenVisR     Genomic Visualizations in R Bioconductor version: Release (3.5) Produce highly customizable publication quality graphics for genomic data primarily at the cohort level. Author: Zachary Skidmore [aut, cre], Alex Wagner [aut], Robert Lesurf [aut], Katie Campbell [aut], Jason Kunisaki [aut], Obi Griffith [aut], Malachi Griffith [aut] Maintainer:…

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Bioconductor – edgeR

DOI: 10.18129/B9.bioc.edgeR     Empirical Analysis of Digital Gene Expression Data in R Bioconductor version: Release (3.5) Differential expression analysis of RNA-seq expression profiles with biological replication. Implements a range of statistical methodology based on the negative binomial distributions, including empirical Bayes estimation, exact tests, generalized linear models and quasi-likelihood…

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Bioconductor – globaltest

Testing groups of covariates/features for association with a response variable, with applications to gene set testing Bioconductor version: 2.5 The global test tests groups of covariates (or features) for association with a response variable. This package implements the test with diagnostic plots and multiple testing utilities, along with several functions…

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Bioconductor – coGPS

    This package is for version 3.0 of Bioconductor; for the stable, up-to-date release version, see coGPS. cancer outlier Gene Profile Sets Bioconductor version: 3.0 Gene Set Enrichment Analysis of P-value based statistics for outlier gene detection in dataset merged from multiple studies Author: Yingying Wei, Michael Ochs Maintainer:…

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How can I annotate microarray data set through Ensemble Id?

Hi, I am studying on microarray data set which its platform is the GPL 96([HG-U133A] ). Consequently, I used the GPL 96 annotation file to annotate gene expression data and convert probe ids into gene identifiers. My problem is that in the annotation file I see three columns as gene…

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Bioconductor – PathNetData

    This package is for version 2.13 of Bioconductor; for the stable, up-to-date release version, see PathNetData. Experimental data for the PathNet package Bioconductor version: 2.13 This package contains the data employed in the vignette of the PathNet package. These data belong to the following publication: PathNet: A tool…

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Bioconductor – MmPalateMiRNA

    This package is for version 2.13 of Bioconductor; for the stable, up-to-date release version, see MmPalateMiRNA. Murine Palate miRNA Expression Analysis Bioconductor version: 2.13 R package compendium for the analysis of murine palate miRNA two-color expression data. Author: Guy Brock <guy.brock at louisville.edu>, Partha Mukhopadhyay <p0mukh01 at louisville.edu>,…

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Bioconductor – SSPA

    This package is for version 3.0 of Bioconductor; for the stable, up-to-date release version, see SSPA. General Sample Size and Power Analysis for Microarray and Next-Generation Sequencing Data Bioconductor version: 3.0 General Sample size and power analysis for microarray and next-generation sequencing data. Author: Maarten van Iterson Maintainer:…

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NFP: Network fingerprint analysis in R

This package implements the network fingerprint framework. A biomedical network is characterized as a spectrum-like vector called “network fingerprint”, which contains similarities to basic networks. This knowledge-based multidimensional characterization provides a more intuitive way to decipher molecular networks, especially for large-scale network comparisons and clustering analyses Prerequisites NFP is free…

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Bioconductor – svaRetro

DOI: 10.18129/B9.bioc.svaRetro     Retrotransposed transcript detection from structural variants Bioconductor version: Release (3.14) svaRetro contains functions for detecting retrotransposed transcripts (RTs) from structural variant calls. It takes structural variant calls in GRanges of breakend notation and identifies RTs by exon-exon junctions and insertion sites. The candidate RTs are reported…

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Bioconductor – cytofast

DOI: 10.18129/B9.bioc.cytofast     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 cytofast. cytofast…

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Bioconductor – msPurity

DOI: 10.18129/B9.bioc.msPurity     Automated Evaluation of Precursor Ion Purity for Mass Spectrometry Based Fragmentation in Metabolomics Bioconductor version: Release (3.5) Assess the contribution of the targeted precursor in fragmentation acquired or anticipated isolation windows using a metric called “precursor purity”. Also provides simple processing steps (averaging, filtering, blank subtraction,…

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Bioconductor – pRoloc

    This package is for version 3.0 of Bioconductor; for the stable, up-to-date release version, see pRoloc. A unifying bioinformatics framework for spatial proteomics Bioconductor version: 3.0 This package implements pattern recognition techniques on quantitiative mass spectrometry data to infer protein sub-cellular localisation. Author: Laurent Gatto and Lisa M….

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Bioconductor – netresponse

    This package is for version 2.12 of Bioconductor; for the stable, up-to-date release version, see netresponse. NetResponse: functional network analysis Bioconductor version: 2.12 Algorithms for functional network analysis. Includes an implementation of a variational Dirichlet process Gaussian mixture model for nonparametric mixture modeling. Author: Leo Lahti, Olli-Pekka Huovilainen,…

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Bioconductor – dStruct

DOI: 10.18129/B9.bioc.dStruct     Identifying differentially reactive regions from RNA structurome profiling data Bioconductor version: Release (3.14) dStruct identifies differentially reactive regions from RNA structurome profiling data. dStruct is compatible with a broad range of structurome profiling technologies, e.g., SHAPE-MaP, DMS-MaPseq, Structure-Seq, SHAPE-Seq, etc. See Choudhary et al, Genome Biology,…

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bioinformatics-ua/DrAC – Giters

DrAC – Drug Annotator for Common data model A solution for extracting Patients’ information from clinical notes and exporting it to an OMOP CDM database. New Features! Annotate medication information in clinical notes Harmonise the resulting information into their standard definition Store extracted drug information into the OMOP CDM Documentation…

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Bioconductor – BeadDataPackR

    This package is for version 2.12 of Bioconductor; for the stable, up-to-date release version, see BeadDataPackR. Compression of Illumina BeadArray data Bioconductor version: 2.12 Provides functionality for the compression and decompression of raw bead-level data from the Illumina BeadArray platform Author: Mike Smith, Andy Lynch Maintainer: Mike Smith…

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Bioconductor – rBiopaxParser

    This package is for version 3.3 of Bioconductor; for the stable, up-to-date release version, see rBiopaxParser. Parses BioPax files and represents them in R Bioconductor version: 3.3 Parses BioPAX files and represents them in R, at the moment BioPAX level 2 and level 3 are supported. Author: Frank…

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Bioconductor – IntramiRExploreR

DOI: 10.18129/B9.bioc.IntramiRExploreR     This package is for version 3.7 of Bioconductor; for the stable, up-to-date release version, see IntramiRExploreR. Predicting Targets for Drosophila Intragenic miRNAs Bioconductor version: 3.7 Intra-miR-ExploreR, an integrative miRNA target prediction bioinformatics tool, identifies targets combining expression and biophysical interactions of a given microRNA (miR). Using…

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the standard deviation is zero”

Hi, I am following RnBeads tutorial and with Ziller2011_PLoSGen_450K data set. The tutorial says that the analysis takes 1 1/2 hours on two compute nodes but for me after overnight run with 4 cores it didn’t finish so I had to terminate the process. It seems that there is a…

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Bioconductor – cageminer

DOI: 10.18129/B9.bioc.cageminer     Candidate Gene Miner Bioconductor version: Release (3.14) This package aims to integrate GWAS-derived SNPs and coexpression networks to mine candidate genes associated with a particular phenotype. For that, users must define a set of guide genes, which are known genes involved in the studied phenotype. Additionally,…

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Forcing Rstudio to use a specific version of R on linux

Meta Stack Overflow ,Stack Overflow en español,Stack Overflow em Português, Stack Overflow Public questions & answers load more v I have installed an older R version using the source on a mac, but I am finding it difficult to get Rstudio to see this version. Is there an easy way…

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Bioconductor – BgeeCall

DOI: 10.18129/B9.bioc.BgeeCall     This package is for version 3.12 of Bioconductor; for the stable, up-to-date release version, see BgeeCall. Automatic RNA-Seq present/absent gene expression calls generation Bioconductor version: 3.12 BgeeCall allows to generate present/absent gene expression calls without using an arbitrary cutoff like TPM Author: Julien Wollbrett [aut, cre],…

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Bioconductor – MetaboSignal (development version)

DOI: 10.18129/B9.bioc.MetaboSignal     This is the development version of MetaboSignal; for the stable release version, see MetaboSignal. MetaboSignal: a network-based approach to overlay and explore metabolic and signaling KEGG pathways Bioconductor version: Development (3.15) MetaboSignal is an R package that allows merging, analyzing and customizing metabolic and signaling KEGG…

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Bioconductor – leukemiasEset

DOI: 10.18129/B9.bioc.leukemiasEset     This package is for version 3.8 of Bioconductor; for the stable, up-to-date release version, see leukemiasEset. Leukemia’s microarray gene expression data (expressionSet). Bioconductor version: 3.8 Expressionset containing gene expresion data from 60 bone marrow samples of patients with one of the four main types of leukemia…

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Bioconductor – TRESS

DOI: 10.18129/B9.bioc.TRESS     Toolbox for mRNA epigenetics sequencing analysis Bioconductor version: Release (3.14) This package is devoted to analyzing MeRIP-seq data. Current functionality is for detection of transcriptome-wide m6A methylation regions. The method is based on hierarchical negative binomial models. Author: Zhenxing Guo [aut, cre], Hao Wu [ctb] Maintainer:…

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LAMMPS Patch Release 27 October 2021

LAMMPS Patch Release Overview What is LAMMPS used for? LAMMPS is a classical molecular dynamics (MD) code that models ensembles of particles in a liquid, solid, or gaseous state. It can model atomic, polymeric, biological, solid-state (metals, ceramics, oxides), granular, coarse-grained, or macroscopic systems using a variety of interatomic potentials…

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Bioconductor – ImpulseDE

    This package is for version 3.4 of Bioconductor; for the stable, up-to-date release version, see ImpulseDE. Detection of DE genes in time series data using impulse models Bioconductor version: 3.4 ImpulseDE is suited to capture single impulse-like patterns in high throughput time series datasets. By fitting a representative…

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How to annotate GPL for GEO data byhand?

How to annotate GPL for GEO data byhand? 1 Hello, getGEO() function always fail to AnnoGPL for GSE69644. Error because 1: In download.file(myurl, destfile, mode = mode, quiet = TRUE, method = getOption(“download.file.method.GEOquery”)) : cannot open URL ‘https://ftp.ncbi.nlm.nih.gov/geo/platforms/GPL13nnn/GPL13667/annot/GPL13667.annot.gz’: HTTP status was ‘404 Not Found’ I want to know how can…

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Bioconductor – ADaCGH2

    This package is for version 2.12 of Bioconductor; for the stable, up-to-date release version, see ADaCGH2. Analysis of data from aCGH experiments using parallel computing and ff objects Bioconductor version: 2.12 Analysis and plotting of array CGH data. Allows usage of Circular Binary Segementation, wavelet-based smoothing (both as…

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Bioconductor – BioNet

    This package is for version 3.3 of Bioconductor; for the stable, up-to-date release version, see BioNet. Routines for the functional analysis of biological networks Bioconductor version: 3.3 This package provides functions for the integrated analysis of protein-protein interaction networks and the detection of functional modules. Different datasets can…

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Bioconductor – scDataviz

DOI: 10.18129/B9.bioc.scDataviz     This package is for version 3.12 of Bioconductor; for the stable, up-to-date release version, see scDataviz. scDataviz: single cell dataviz and downstream analyses Bioconductor version: 3.12 In the single cell World, which includes flow cytometry, mass cytometry, single-cell RNA-seq (scRNA-seq), and others, there is a need…

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Bioconductor – target

DOI: 10.18129/B9.bioc.target     This package is for version 3.10 of Bioconductor; for the stable, up-to-date release version, see target. Predict Combined Function of Transcription Factors Bioconductor version: 3.10 Implement the BETA algorithm for infering direct target genes from DNA-binding and perturbation expression data Wang et al. (2013) . Extend…

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435.gromacs: SPEC CPU2006 Benchmark Description

435.gromacs: SPEC CPU2006 Benchmark Description Benchmark Name 435.gromacs Benchmark Author Erik Lindahl <lindahl [at] gromacs.org>Department of Structural BiologyStockholm Bioinformatics CentreStockholmSweden David van der Spoel <spoel [at] gromacs.org>Department of BiochemistryUppsala UniversityBox 576, 751 23 UppsalaSWEDEN Benchmark Program General Category Chemistry / Molecular Dynamics Benchmark Description 435.gromacs is derived from GROMACS, a…

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Bioconductor – esATAC

DOI: 10.18129/B9.bioc.esATAC     This package is for version 3.12 of Bioconductor; for the stable, up-to-date release version, see esATAC. An Easy-to-use Systematic pipeline for ATACseq data analysis Bioconductor version: 3.12 This package provides a framework and complete preset pipeline for quantification and analysis of ATAC-seq Reads. It covers raw…

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interesting kaggle datasets

Kaggle ARC challenge has set May 27 as the final submission deadline for the ARC challenge. Kaggle Datasets. The internet is a treasure trove of valuable information for aspiring data scientists. • updated 2 years ago (Version 3) Data Tasks Code (1,473) Discussion (1) Activity Metadata. (Some might need you…

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Bioconductor – rGREAT

    This package is for version 3.2 of Bioconductor; for the stable, up-to-date release version, see rGREAT. Client for GREAT Analysis Bioconductor version: 3.2 This package makes GREAT (Genomic Regions Enrichment of Annotations Tool) analysis automatic by constructing a HTTP POST request according to user’s input and automatically retrieving…

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Bioconductor – DMRScan

DOI: 10.18129/B9.bioc.DMRScan     This package is for version 3.10 of Bioconductor; for the stable, up-to-date release version, see DMRScan. Detection of Differentially Methylated Regions Bioconductor version: 3.10 This package detects significant differentially methylated regions (for both qualitative and quantitative traits), using a scan statistic with underlying Poisson heuristics. The…

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Bioconductor – MADSEQ

DOI: 10.18129/B9.bioc.MADSEQ     This package is for version 3.10 of Bioconductor; for the stable, up-to-date release version, see MADSEQ. Mosaic Aneuploidy Detection and Quantification using Massive Parallel Sequencing Data Bioconductor version: 3.10 The MADSEQ package provides a group of hierarchical Bayeisan models for the detection of mosaic aneuploidy, the…

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Bioconductor – Heatplus

DOI: 10.18129/B9.bioc.Heatplus     Heatmaps with row and/or column covariates and colored clusters Bioconductor version: Release (3.6) Display a rectangular heatmap (intensity plot) of a data matrix. By default, both samples (columns) and features (row) of the matrix are sorted according to a hierarchical clustering, and the corresponding dendrogram is…

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Bioconductor – ProteoDisco (development version)

DOI: 10.18129/B9.bioc.ProteoDisco     This is the development version of ProteoDisco; to use it, please install the devel version of Bioconductor. Generation of customized protein variant databases from genomic variants, splice-junctions and manual sequences Bioconductor version: Development (3.14) ProteoDisco is an R package to facilitate proteogenomics studies. It houses functions…

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Bioconductor – proteinProfiles

DOI: 10.18129/B9.bioc.proteinProfiles     Protein Profiling Bioconductor version: Release (3.6) Significance assessment for distance measures of time-course protein profiles Author: Julian Gehring Maintainer: Julian Gehring <jg-bioc at gmx.com> Citation (from within R, enter citation(“proteinProfiles”)): Installation To install this package, start R and enter: ## try http:// if https:// URLs are…

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Bioconductor – nethet

DOI: 10.18129/B9.bioc.nethet     This package is for version 3.11 of Bioconductor; for the stable, up-to-date release version, see nethet. A bioconductor package for high-dimensional exploration of biological network heterogeneity Bioconductor version: 3.11 Package nethet is an implementation of statistical solid methodology enabling the analysis of network heterogeneity from high-dimensional…

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Rbberger Lammps Doc Utils Blob Master Lammpsdoc Doc_anchor_check.pydoc Anchor Macro 182682072.htmlwiki Anchor_

Result for: Rbberger Lammps Doc Utils Blob Master Lammpsdoc Doc_anchor_check.pydoc Anchor Macro 182682072.htmlwiki Anchor_ Rbberger Lammps Doc Utils Blob Master Lammpsdoc Doc_anchor_check.pydoc Anchor Macro 182682072.htmlwiki Anchor_ GitHub – rbberger/lammps-doc-utils: Utilities for … Fri, 27 Aug 2021 01:36:00 GMT – This tool is no longer necessary. All of the LAMMPS documentation…

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Bioconductor – Melissa

DOI: 10.18129/B9.bioc.Melissa     This package is for version 3.9 of Bioconductor; for the stable, up-to-date release version, see Melissa. Bayesian clustering and imputationa of single cell methylomes Bioconductor version: 3.9 Melissa is a Baysian probabilistic model for jointly clustering and imputing single cell methylomes. This is done by taking…

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Bioconductor – PREDA

    This package is for version 3.0 of Bioconductor; for the stable, up-to-date release version, see PREDA. Position RElated Data Anlysis Bioconductor version: 3.0 Package for the position related analysis of quantitative functional genomics data. Author: Francesco Ferrari <francesco.ferrari at unimore.it> Maintainer: Francesco Ferrari <francesco.ferrari at unimore.it> Citation (from…

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Bioconductor – netprioR

    This package is for version 3.4 of Bioconductor; for the stable, up-to-date release version, see netprioR. A model for network-based prioritisation of genes Bioconductor version: 3.4 A model for semi-supervised prioritisation of genes integrating network data, phenotypes and additional prior knowledge about TP and TN gene labels from…

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Bioconductor – eisa

    This package is for version 2.9 of Bioconductor; for the stable, up-to-date release version, see eisa. Expression data analysis via the Iterative Signature Algorithm Bioconductor version: 2.9 The Iterative Signature Algorithm (ISA) is a biclustering method; it finds correlated blocks (transcription modules) in gene expression (or other tabular)…

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Bioconductor – rgsepd

    This package is for version 3.4 of Bioconductor; for the stable, up-to-date release version, see rgsepd. Gene Set Enrichment / Projection Displays Bioconductor version: 3.4 R/GSEPD is a bioinformatics package for R to help disambiguate transcriptome samples (a matrix of RNA-Seq counts at RefSeq IDs) by automating differential…

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Bioconductor – GeneGA

    This package is for version 2.9 of Bioconductor; for the stable, up-to-date release version, see GeneGA. Design gene based on both mRNA secondary structure and codon usage bias using Genetic algorithm Bioconductor version: 2.9 R based Genetic algorithm for gene expression optimization by considering both mRNA secondary structure…

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Bioconductor – Harman

DOI: 10.18129/B9.bioc.Harman     This package is for version 3.12 of Bioconductor; for the stable, up-to-date release version, see Harman. The removal of batch effects from datasets using a PCA and constrained optimisation based technique Bioconductor version: 3.12 Harman is a PCA and constrained optimisation based technique that maximises the…

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Bioconductor – ERSSA

DOI: 10.18129/B9.bioc.ERSSA     This package is for version 3.9 of Bioconductor; for the stable, up-to-date release version, see ERSSA. Empirical RNA-seq Sample Size Analysis Bioconductor version: 3.9 The ERSSA package takes user supplied RNA-seq differential expression dataset and calculates the number of differentially expressed genes at varying biological replicate…

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Bioconductor – NBAMSeq

DOI: 10.18129/B9.bioc.NBAMSeq     This package is for version 3.9 of Bioconductor; for the stable, up-to-date release version, see NBAMSeq. Negative Binomial Additive Model for RNA-Seq Data Bioconductor version: 3.9 High-throughput sequencing experiments followed by differential expression analysis is a widely used approach to detect genomic biomarkers. A fundamental step…

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Bioconductor – FunciSNP

DOI: 10.18129/B9.bioc.FunciSNP     This package is for version 3.11 of Bioconductor; for the stable, up-to-date release version, see FunciSNP. Integrating Functional Non-coding Datasets with Genetic Association Studies to Identify Candidate Regulatory SNPs Bioconductor version: 3.11 FunciSNP integrates information from GWAS, 1000genomes and chromatin feature to identify functional SNP in…

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Bioconductor – ChIPComp

    This package is for version 3.4 of Bioconductor; for the stable, up-to-date release version, see ChIPComp. Quantitative comparison of multiple ChIP-seq datasets Bioconductor version: 3.4 ChIPComp detects differentially bound sharp binding sites across multiple conditions considering matching control. Author: Hao Wu, Li Chen, Zhaohui S.Qin, Chi Wang Maintainer:…

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Bioconductor – MotIV

    This package is for version 3.4 of Bioconductor; for the stable, up-to-date release version, see MotIV. Motif Identification and Validation Bioconductor version: 3.4 This package makes use of STAMP for comparing a set of motifs to a given database (e.g. JASPAR). It can also be used to visualize…

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Bioconductor – GEOexplorer (development version)

DOI: 10.18129/B9.bioc.GEOexplorer     This is the development version of GEOexplorer; to use it, please install the devel version of Bioconductor. GEOexplorer: an R/Bioconductor package for gene expression analysis and visualisation Bioconductor version: Development (3.14) GEOexplorer is a Shiny app that enables exploratory data analysis and differential gene expression of…

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Bioconductor – GRENITS

    This package is for version 2.14 of Bioconductor; for the stable, up-to-date release version, see GRENITS. Gene Regulatory Network Inference Using Time Series Bioconductor version: 2.14 The package offers four network inference statistical models using Dynamic Bayesian Networks and Gibbs Variable Selection: a linear interaction model, two linear…

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Bioconductor – Clomial

DOI: 10.18129/B9.bioc.Clomial     This package is for version 3.12 of Bioconductor; for the stable, up-to-date release version, see Clomial. Infers clonal composition of a tumor Bioconductor version: 3.12 Clomial fits binomial distributions to counts obtained from Next Gen Sequencing data of multiple samples of the same tumor. The trained…

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Bioconductor – MSGFgui

DOI: 10.18129/B9.bioc.MSGFgui     A shiny GUI for MSGFplus Bioconductor version: Release (3.5) This package makes it possible to perform analyses using the MSGFplus package in a GUI environment. Furthermore it enables the user to investigate the results using interactive plots, summary statistics and filtering. Lastly it exposes the current…

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Bioconductor – wateRmelon

DOI: 10.18129/B9.bioc.wateRmelon     This package is for version 3.11 of Bioconductor; for the stable, up-to-date release version, see wateRmelon. Illumina 450 methylation array normalization and metrics Bioconductor version: 3.11 15 flavours of betas and three performance metrics, with methods for objects produced by methylumi and minfi packages. Author: Leonard…

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Bioconductor – conclus

DOI: 10.18129/B9.bioc.conclus     ScRNA-seq Workflow CONCLUS – From CONsensus CLUSters To A Meaningful CONCLUSion Bioconductor version: Release (3.13) CONCLUS is a tool for robust clustering and positive marker features selection of single-cell RNA-seq (sc-RNA-seq) datasets. It takes advantage of a consensus clustering approach that greatly simplify sc-RNA-seq data analysis…

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Bioconductor – FoldGO

DOI: 10.18129/B9.bioc.FoldGO     Package for Fold-specific GO Terms Recognition Bioconductor version: Release (3.13) FoldGO is a package designed to annotate gene sets derived from expression experiments and identify fold-change-specific GO terms. Author: Daniil Wiebe <daniil.wiebe at gmail.com> [aut, cre] Maintainer: Daniil Wiebe <daniil.wiebe at gmail.com> Citation (from within R,…

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Bioconductor – tRNAdbImport

DOI: 10.18129/B9.bioc.tRNAdbImport     Importing from tRNAdb and mitotRNAdb as GRanges objects Bioconductor version: Release (3.13) tRNAdbImport imports the entries of the tRNAdb and mtRNAdb (trna.bioinf.uni-leipzig.de) as GRanges object. Author: Felix G.M. Ernst [aut, cre] Maintainer: Felix G.M. Ernst <felix.gm.ernst at outlook.com> Citation (from within R, enter citation(“tRNAdbImport”)): Installation To…

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Bioconductor – geecc

DOI: 10.18129/B9.bioc.geecc     This package is for version 3.11 of Bioconductor. This package has been removed from Bioconductor. For the last stable, up-to-date release version, see geecc. Gene Set Enrichment Analysis Extended to Contingency Cubes Bioconductor version: 3.11 Use log-linear models to perform hypergeometric and chi-squared tests for gene…

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Bioconductor – marr

DOI: 10.18129/B9.bioc.marr     Maximum rank reproducibility Bioconductor version: Release (3.13) marr (Maximum Rank Reproducibility) is a nonparametric approach that detects reproducible signals using a maximal rank statistic for high-dimensional biological data. In this R package, we implement functions that measures the reproducibility of features per sample pair and sample…

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GPL arguments in getGEO()

GPL arguments in getGEO() 0 Hi, I’ve been trying to get GEO data using the getGEO() function and I was wondering what do the arguments AnnotGPL and getGPL do exactly? I tried setting them to T or F and then comparing the output but I don’t observe any differences, am…

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Bioconductor – MethPed

    This package is for version 3.4 of Bioconductor; for the stable, up-to-date release version, see MethPed. A DNA methylation classifier tool for the identification of pediatric brain tumor subtypes Bioconductor version: 3.4 Classification of pediatric tumors into biologically defined subtypes is challenging and multifaceted approaches are needed. For…

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Bioconductor – DuoClustering2018 (development version)

DOI: 10.18129/B9.bioc.DuoClustering2018     This is the development version of DuoClustering2018; for the stable release version, see DuoClustering2018. Data, Clustering Results and Visualization Functions From Duò et al (2018) Bioconductor version: Development (3.14) Preprocessed experimental and simulated scRNA-seq data sets used for evaluation of clustering methods for scRNA-seq data in…

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Bioconductor – unifiedWMWqPCR

DOI: 10.18129/B9.bioc.unifiedWMWqPCR     This package is for version 3.11 of Bioconductor; for the stable, up-to-date release version, see unifiedWMWqPCR. Unified Wilcoxon-Mann Whitney Test for testing differential expression in qPCR data Bioconductor version: 3.11 This packages implements the unified Wilcoxon-Mann-Whitney Test for qPCR data. This modified test allows for testing…

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Bioconductor – cageminer (development version)

DOI: 10.18129/B9.bioc.cageminer     This is the development version of cageminer; to use it, please install the devel version of Bioconductor. Candidate Gene Miner Bioconductor version: Development (3.14) This package aims to integrate GWAS-derived SNPs and coexpression networks to mine candidate genes associated with a particular phenotype. For that, users…

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Predicting and characterizing a cancer dependency map of tumors with deep learning

INTRODUCTION The development of novel cancer therapies requires knowledge of specific biological pathways to target individual tumors and eradicate cancer cells. Toward this goal, the landscape of genetic vulnerabilities of cancer, or the cancer dependency map, is being systematically profiled. Using RNA interference (RNAi) loss-of-function screens, Marcotte et al. (1),…

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Bioconductor – aCGH

    This package is for version 2.9 of Bioconductor; for the stable, up-to-date release version, see aCGH. Classes and functions for Array Comparative Genomic Hybridization data. Bioconductor version: 2.9 Functions for reading aCGH data from image analysis output files and clone information files, creation of aCGH S3 objects for…

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Analysing RNA seq data

Analysing RNA seq data 1 Hello all! I am new analysing RNA-seq data. They give me a directory containing: 1 normal sample and 15 tumor samples, each one has its cel file, exp file, and dcl file. They ask me to do a reanalysis, but I think I need more…

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Strange difference in the order of probe ID between my matrix from cel and the series matrix the author uploaded

Hi all,I met a very strange error when reading and doing RMA of the raw cel files. When i use the following codes to do the background correction and normalization of GSE18997 (platform GPL570), I found the order of some probe IDs of the final results seems to be different…

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