Tag: GPL

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 – 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 – 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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mysql – Trying to Authenticate the Slurm User via Keys Instead of Password Using the pam Plugin on MariaDB

mysql – Trying to Authenticate the Slurm User via Keys Instead of Password Using the pam Plugin on MariaDB – Database Administrators Stack Exchange Stack Exchange Network Stack Exchange network consists of 183 Q&A communities including Stack Overflow, the largest, most trusted online community for developers to learn, share their…

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Accessing Snowflake with R Studio via ODBC on SPCS | by Gabriel Mullen | Snowflake | Dec, 2023

In a previous post, I was able to deploy a R Studio container into Snowpark Container Service. This allows me to run R code directly in Snowflake, but I still need to connect to Snowflake to grab data. So when I attempted to use the dbConnect syntax from the original…

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drivers/power/wm97xx_battery.c – kernel/tegra.git – Git at Google

/* * linux/drivers/power/wm97xx_battery.c * * Battery measurement code for WM97xx * * based on tosa_battery.c * * Copyright (C) 2008 Marek Vasut <marek.vasut@gmail.com> * * This program is free software; you can redistribute it and/or modify * it under the terms of the GNU General Public License version 2 as…

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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 – 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 – 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 – 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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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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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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#1056648 – ITP: r-cran-ggstats — GNU R extension to ‘ggplot2’ for plotting stats

#1056648 – ITP: r-cran-ggstats — GNU R extension to ‘ggplot2’ for plotting stats – Debian Bug report logs Reply or subscribe to this bug. Toggle useless messages Report forwarded to debian-bugs-dist@lists.debian.org, r-pkg-team@alioth-lists.debian.net, wnpp@debian.org:Bug#1056648; Package wnpp. (Fri, 24 Nov 2023 11:00:03 GMT) (full text, mbox, link). Acknowledgement sent to Andreas Tille…

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r-cran-ggstats — GNU R extension to ‘ggplot2’ for plotting stats

Package: wnpp Severity: wishlist Subject: ITP: r-cran-ggstats — GNU R extension to ‘ggplot2’ for plotting stats Package: wnpp Owner: Andreas Tille <ti…@debian.org> Severity: wishlist * Package name : r-cran-ggstats Version : 0.5.1 Upstream Author : Joseph Larmarange * URL : cran.r-project.org/package=ggstats * License : GPL-3+ Programming Lang: GNU R Description…

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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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Bioconductor – CAGEr

DOI: 10.18129/B9.bioc.CAGEr     This package is for version 3.9 of Bioconductor; for the stable, up-to-date release version, see CAGEr. Analysis of CAGE (Cap Analysis of Gene Expression) sequencing data for precise mapping of transcription start sites and promoterome mining Bioconductor version: 3.9 Preprocessing of CAGE sequencing data, identification and…

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Bioconductor – CountClust

DOI: 10.18129/B9.bioc.CountClust     This package is for version 3.10 of Bioconductor; for the stable, up-to-date release version, see CountClust. Clustering and Visualizing RNA-Seq Expression Data using Grade of Membership Models Bioconductor version: 3.10 Fits grade of membership models (GoM, also known as admixture models) to cluster RNA-seq gene expression…

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Bioconductor – tspair

DOI: 10.18129/B9.bioc.tspair     This package is for version 3.12 of Bioconductor; for the stable, up-to-date release version, see tspair. Top Scoring Pairs for Microarray Classification Bioconductor version: 3.12 These functions calculate the pair of genes that show the maximum difference in ranking between two user specified groups. This “top…

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Bioconductor – agilp

    This package is for version 2.11 of Bioconductor; for the stable, up-to-date release version, see agilp. Agilent expression array processing package Bioconductor version: 2.11 provides a pipeline for the low-level analysis of gene expression microarray data, primarily Agilent data Author: Benny Chain <b.chain at ucl.ac.uk> Maintainer: Benny Chain…

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Bioconductor – TCGAbiolinks

DOI: 10.18129/B9.bioc.TCGAbiolinks     TCGAbiolinks: An R/Bioconductor package for integrative analysis with GDC data Bioconductor version: Release (3.5) The aim of TCGAbiolinks is : i) facilitate the GDC open-access data retrieval, ii) prepare the data using the appropriate pre-processing strategies, iii) provide the means to carry out different standard analyses…

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Bioconductor – ReactomePA

    This package is for version 2.12 of Bioconductor; for the stable, up-to-date release version, see ReactomePA. Reactome Pathway Analysis Bioconductor version: 2.12 This package provides functions for pathway analysis based on REACTOME pathway database. It will implement enrichment analysis, gene set enrichment analysis and functional modules detection. Author:…

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Bioconductor – iCOBRA

DOI: 10.18129/B9.bioc.iCOBRA     Comparison and Visualization of Ranking and Assignment Methods Bioconductor version: Release (3.6) This package provides functions for calculation and visualization of performance metrics for evaluation of ranking and binary classification (assignment) methods. It also contains a shiny application for interactive exploration of results. Author: Charlotte Soneson…

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Bioconductor – receptLoss

DOI: 10.18129/B9.bioc.receptLoss   Unsupervised Identification of Genes with Expression Loss in Subsets of Tumors Bioconductor version: Release (3.18) receptLoss identifies genes whose expression is lost in subsets of tumors relative to normal tissue. It is particularly well-suited in cases where the number of normal tissue samples is small, as the…

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Bioconductor – CDI

DOI: 10.18129/B9.bioc.CDI   Clustering Deviation Index (CDI) Bioconductor version: Release (3.18) Single-cell RNA-sequencing (scRNA-seq) is widely used to explore cellular variation. The analysis of scRNA-seq data often starts from clustering cells into subpopulations. This initial step has a high impact on downstream analyses, and hence it is important to be…

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How to install or uninstall “sagemath-data-combinatorial_designs.noarch” on Fedora 35 ?

1. Install sagemath-data-combinatorial_designs.noarch package Please follow the step by step instructions below to install sagemath-data-combinatorial_designs.noarch package: sudo dnf install sagemath-data-combinatorial_designs.noarch Copy 2. Uninstall / Remove sagemath-data-combinatorial_designs.noarch package Please follow the steps below to uninstall sagemath-data-combinatorial_designs.noarch package: sudo dnf remove sagemath-data-combinatorial_designs.noarch Copy 3. Details of sagemath-data-combinatorial_designs.noarch package Last metadata expiration check:…

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Bioconductor – SEtools

DOI: 10.18129/B9.bioc.SEtools     This package is for version 3.12 of Bioconductor; for the stable, up-to-date release version, see SEtools. SEtools: tools for working with SummarizedExperiment Bioconductor version: 3.12 This includes a set of tools for working with the SummarizedExperiment class, including merging, melting, aggregation and plotting functions. In particular,…

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Bioconductor – ResidualMatrix

DOI: 10.18129/B9.bioc.ResidualMatrix   Creating a DelayedMatrix of Regression Residuals Bioconductor version: Release (3.18) Provides delayed computation of a matrix of residuals after fitting a linear model to each column of an input matrix. Also supports partial computation of residuals where selected factors are to be preserved in the output matrix….

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Bioconductor – mariner (development version)

DOI: 10.18129/B9.bioc.mariner   This is the development version of mariner; for the stable release version, see mariner. Mariner: Explore the Hi-Cs Bioconductor version: Development (3.19) Tools for manipulating paired ranges and working with Hi-C data in R. Functionality includes manipulating/merging paired regions, generating paired ranges, extracting/aggregating interactions from `.hic` files,…

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Bioconductor – genomes

DOI: 10.18129/B9.bioc.genomes     This package is for version 3.9 of Bioconductor; for the stable, up-to-date release version, see genomes. Genome sequencing project metadata Bioconductor version: 3.9 Download genome and assembly reports from NCBI Author: Chris Stubben Maintainer: Chris Stubben <stubben at lanl.gov> Citation (from within R, enter citation(“genomes”)): Installation…

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Bioconductor – Rvisdiff

DOI: 10.18129/B9.bioc.Rvisdiff   Interactive Graphs for Differential Expression Bioconductor version: Release (3.18) Creates a muti-graph web page which allows the interactive exploration of differential expression results. The graphical web interface presents results as a table which is integrated with five interactive graphs: MA-plot, volcano plot, box plot, lines plot and…

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Bioconductor – scider (development version)

DOI: 10.18129/B9.bioc.scider   This is the development version of scider; to use it, please install the devel version of Bioconductor. Spatial cell-type inter-correlation by density in R Bioconductor version: Development (3.18) scider is an user-friendly R package providing functions to model the global density of cells in a slide of…

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r – Using a dataframe name from the dataframes list in the axis name in a ggplot plot

I have a list of data frames Based on this, I prepare ggplot charts co_gpl <- lapply(co_lst, function(x) { ggplot(x) + geom_line (aes (x = `Czas`, y = get(names(x[grep(“Temp. zasilania”, colnames (x))])) ), color = “red3”, size = 0.3) + geom_line (aes (x = `Czas`, y = get(names(x[grep(“Temp. powrotu”, colnames…

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OrthoMCL installation on Ubuntu Linux

About OrthoMCL OrthoMCL is a software used for assigning proteomes to ortholog groups. About this tutorial These are the steps I followed to install OrthoMCL on an Ubuntu 14.04 Linux server using MySQL as the database system. Requirements Ubuntu 14.04 (tested). Might work on other versions. All these steps are…

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Arch Linux – sagemath 10.1-7 (x86_64)

sagemath 10.1-7 Architecture: x86_64 Repository: Extra Description: Open Source Mathematics Software, free alternative to Magma, Maple, Mathematica, and Matlab Upstream URL: www.sagemath.org License(s): GPL Replaces: sagemath-jupyter Conflicts: sagemath-jupyter Maintainers: Antonio Rojas Package Size: 54.3 MB Installed Size: 496.7 MB Last Packager: Antonio Rojas Build Date: 2023-10-22 09:07 UTC Signed By: Antonio Rojas…

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Is it possible to get taxonomy identifiers from diamond output without using –taxonmap during makedb?

Is it possible to get taxonomy identifiers from diamond output without using –taxonmap during makedb? 1 I want to run diamond and also get taxon identifiers for each hit. Is the only way to do this by incorporating it during the makedb step? Is there any other option? The reason…

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Bioconductor – dagLogo

DOI: 10.18129/B9.bioc.dagLogo     This package is for version 3.15 of Bioconductor; for the stable, up-to-date release version, see dagLogo. dagLogo: a Bioconductor package for visualizing conserved amino acid sequence pattern in groups based on probability theory Bioconductor version: 3.15 Visualize significant conserved amino acid sequence pattern in groups based…

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Bioconductor – nipalsMCIA (development version)

DOI: 10.18129/B9.bioc.nipalsMCIA   This is the development version of nipalsMCIA; to use it, please install the devel version of Bioconductor. Multiple Co-Inertia Analysis via the NIPALS Method Bioconductor version: Development (3.18) Computes Multiple Co-Inertia Analysis (MCIA), a dimensionality reduction (jDR) algorithm, for a multi-block dataset using a modification to the…

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Bioconductor – DepInfeR (development version)

DOI: 10.18129/B9.bioc.DepInfeR   This is the development version of DepInfeR; for the stable release version, see DepInfeR. Inferring tumor-specific cancer dependencies through integrating ex-vivo drug response assays and drug-protein profiling Bioconductor version: Development (3.18) DepInfeR integrates two experimentally accessible input data matrices: the drug sensitivity profiles of cancer cell lines…

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Bioconductor – metaboliteIDmapping

DOI: 10.18129/B9.bioc.metaboliteIDmapping     This package is for version 3.14 of Bioconductor; for the stable, up-to-date release version, see metaboliteIDmapping. Mapping of Metabolite IDs from Different Sources Bioconductor version: 3.14 The package provides a comprehensive mapping table of nine different Metabolite ID formats and their common name. The data has…

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Bioconductor – ABAEnrichment

DOI: 10.18129/B9.bioc.ABAEnrichment     This package is for version 3.11 of Bioconductor; for the stable, up-to-date release version, see ABAEnrichment. Gene expression enrichment in human brain regions Bioconductor version: 3.11 The package ABAEnrichment is designed to test for enrichment of user defined candidate genes in the set of expressed genes…

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drivers/extcon/extcon-gpio.c – linux-imx – Git at Google

/* * extcon_gpio.c – Single-state GPIO extcon driver based on extcon class * * Copyright (C) 2008 Google, Inc. * Author: Mike Lockwood <lockwood@android.com> * * Modified by MyungJoo Ham <myungjoo.ham@samsung.com> to support extcon * (originally switch class is supported) * * This software is licensed under the terms of…

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Bioconductor – PAST

DOI: 10.18129/B9.bioc.PAST   Pathway Association Study Tool (PAST) Bioconductor version: Release (3.17) PAST takes GWAS output and assigns SNPs to genes, uses those genes to find pathways associated with the genes, and plots pathways based on significance. Implements methods for reading GWAS input data, finding genes associated with SNPs, calculating…

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Bioconductor – MouseFM

DOI: 10.18129/B9.bioc.MouseFM   In-silico methods for genetic finemapping in inbred mice Bioconductor version: Release (3.17) This package provides methods for genetic finemapping in inbred mice by taking advantage of their very high homozygosity rate (>95%). Author: Matthias Munz [aut, cre] , Inken Wohlers [aut] , Hauke Busch [aut] Maintainer: Matthias…

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Bioconductor – ClusterSignificance

DOI: 10.18129/B9.bioc.ClusterSignificance     The ClusterSignificance package provides tools to assess if class clusters in dimensionality reduced data representations have a separation different from permuted data Bioconductor version: Release (3.11) The ClusterSignificance package provides tools to assess if class clusters in dimensionality reduced data representations have a separation different from…

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Bioconductor – CVE

DOI: 10.18129/B9.bioc.CVE     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 3.11 of Bioconductor. This package has been removed from Bioconductor. For the last stable, up-to-date release version, see CVE. Cancer…

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Outreachy internships working with Bioconductor

Copyright © 2023 Outreachy Free to share and remix: Creative Commons CC-BY, except for the individual organization logos, which are property of their respective owners, and any pictures with additional creative commons attributions. The Outreachy website is built with Django, Wagtail, bootstrap and deployed with Dokku. The code is licensed…

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linux/pdata.h at master – linux

/* SPDX-License-Identifier: GPL-2.0-only */ /* * Platform data for Cirrus Logic Madera codecs * * Copyright (C) 2015-2018 Cirrus Logic */ #ifndef MADERA_PDATA_H #define MADERA_PDATA_H #include <linux/kernel.h> #include <linux/regulator/arizona-ldo1.h> #include <linux/regulator/arizona-micsupp.h> #include <linux/regulator/machine.h> #include <sound/madera-pdata.h> #define MADERA_MAX_MICBIAS 4 #define MADERA_MAX_CHILD_MICBIAS 4 #define MADERA_MAX_GPSW 2 struct gpio_desc; struct pinctrl_map; struct madera_codec_pdata;…

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Bioconductor – MBttest

DOI: 10.18129/B9.bioc.MBttest     This package is for version 3.7 of Bioconductor; for the stable, up-to-date release version, see MBttest. Multiple Beta t-Tests Bioconductor version: 3.7 MBttest method was developed from beta t-test method of Baggerly et al(2003). Compared to baySeq (Hard castle and Kelly 2010), DESeq (Anders and Huber…

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Bioconductor – inveRsion

DOI: 10.18129/B9.bioc.inveRsion     This package is for version 3.7 of Bioconductor; for the stable, up-to-date release version, see inveRsion. Inversions in genotype data Bioconductor version: 3.7 Package to find genetic inversions in genotype (SNP array) data. Author: Alejandro Caceres Maintainer: Alejandro Caceres <acaceres at creal.cat> Citation (from within R,…

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Why dbConnect GEOmetadb_demo.sqlite shows some information while dbConnect GEOmetadb.sqlite shows no information

Why dbConnect GEOmetadb_demo.sqlite shows some information while dbConnect GEOmetadb.sqlite shows no information 0 sqlfile_demo <- getSQLiteFile(destdir = “~/bin/Rpack”, destfile = “GEOmetadb.sqlite_demo.gz”,type=”demo”) con <- dbConnect(SQLite(),sqlfile_demo) getBiocPlatformMap(con)[1:5,] output: title gpl bioc_package manufacturer 1 [Maize] Affymetrix Maize Genome Array GPL4032 Affymetrix 2 Agilent-026652 Whole Human Genome Microarray 4x44K v2 (Probe Name version) GPL13497…

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Bioconductor – GWAS.BAYES

DOI: 10.18129/B9.bioc.GWAS.BAYES   Bayesian analysis of Gaussian GWAS data Bioconductor version: Release (3.17) This package is built to perform GWAS analysis using Bayesian techniques. Currently, GWAS.BAYES has functionality for the implementation of BICOSS for Gaussian phenotypes (Williams, J., Ferreira, M. A., and Ji, T. (2022). BICOSS: Bayesian iterative conditional stochastic…

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Bioconductor – TitanCNA

DOI: 10.18129/B9.bioc.TitanCNA     Subclonal copy number and LOH prediction from whole genome sequencing of tumours Bioconductor version: Release (3.13) Hidden Markov model to segment and predict regions of subclonal copy number alterations (CNA) and loss of heterozygosity (LOH), and estimate cellular prevalence of clonal clusters in tumour whole genome…

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Bioconductor – fgga

DOI: 10.18129/B9.bioc.fgga   Hierarchical ensemble method based on factor graph Bioconductor version: Release (3.17) Package that implements the FGGA algorithm. This package provides a hierarchical ensemble method based ob factor graphs for the consistent cross-ontology annotation of protein coding genes. FGGA embodies elements of predicate logic, communication theory, supervised learning…

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Bioconductor – famat

DOI: 10.18129/B9.bioc.famat   Functional analysis of metabolic and transcriptomic data Bioconductor version: Release (3.17) Famat is made to collect data about lists of genes and metabolites provided by user, and to visualize it through a Shiny app. Information collected is: – Pathways containing some of the user’s genes and metabolites…

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Bioconductor – fastreeR (development version)

DOI: 10.18129/B9.bioc.fastreeR   This is the development version of fastreeR; for the stable release version, see fastreeR. Phylogenetic, Distance and Other Calculations on VCF and Fasta Files Bioconductor version: Development (3.18) Calculate distances, build phylogenetic trees or perform hierarchical clustering between the samples of a VCF or FASTA file. Functions…

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Bioconductor – magrene

DOI: 10.18129/B9.bioc.magrene   This package is for version 3.16 of Bioconductor; for the stable, up-to-date release version, see magrene. Motif Analysis In Gene Regulatory Networks Bioconductor version: 3.16 magrene allows the identification and analysis of graph motifs in (duplicated) gene regulatory networks (GRNs), including lambda, V, PPI V, delta, and…

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Bioconductor – debCAM

DOI: 10.18129/B9.bioc.debCAM   Deconvolution by Convex Analysis of Mixtures Bioconductor version: Release (3.17) An R package for fully unsupervised deconvolution of complex tissues. It provides basic functions to perform unsupervised deconvolution on mixture expression profiles by Convex Analysis of Mixtures (CAM) and some auxiliary functions to help understand the subpopulation-specific…

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Bioconductor – Rnits

DOI: 10.18129/B9.bioc.Rnits   This package is for version 3.16 of Bioconductor; for the stable, up-to-date release version, see Rnits. R Normalization and Inference of Time Series data Bioconductor version: 3.16 R/Bioconductor package for normalization, curve registration and inference in time course gene expression data. Author: Dipen P. Sangurdekar <dipen.sangurdekar at…

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Bioconductor – zFPKM

DOI: 10.18129/B9.bioc.zFPKM   This package is for version 3.16 of Bioconductor; for the stable, up-to-date release version, see zFPKM. A suite of functions to facilitate zFPKM transformations Bioconductor version: 3.16 Perform the zFPKM transform on RNA-seq FPKM data. This algorithm is based on the publication by Hart et al., 2013…

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Bioconductor – bamsignals

DOI: 10.18129/B9.bioc.bamsignals   This package is for version 3.16 of Bioconductor; for the stable, up-to-date release version, see bamsignals. Extract read count signals from bam files Bioconductor version: 3.16 This package allows to efficiently obtain count vectors from indexed bam files. It counts the number of reads in given genomic…

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Maven Central: com.guicedee.servlets:guiced-openapi:1.2.1.1-jre17

<dependency> <groupId>com.guicedee.servlets</groupId> <artifactId>guiced-openapi</artifactId> <version>1.2.1.1-jre17</version> </dependency> <?xml version=”1.0″ encoding=”UTF-8″?> <project xsi:schemaLocation=”http://maven.apache.org/POM/4.0.0 maven.apache.org/xsd/maven-4.0.0.xsd” xmlns=”http://maven.apache.org/POM/4.0.0″ xmlns:xsi=”http://www.w3.org/2001/XMLSchema-instance”> <modelVersion>4.0.0</modelVersion> <groupId>com.guicedee.servlets</groupId> <artifactId>guiced-openapi</artifactId> <version>1.2.1.1-jre17</version> <name>Guiced Swagger</name> <description>Loads Swagger with Guice</description> <url>github.com/GedMarc/GuicedSwagger</url&gt; <licenses> <license> <name>GPL 3</name> <url>www.gnu.org/licenses/gpl-3.0.en.html</url&gt; <distribution>repo</distribution> </license> </licenses> <developers> <developer> <id>GedMarc</id> <name>Marc Magon</name> <email>marc.magon@gmail.com</email> <url>github.com/GedMarc</url&gt; </developer> </developers> <scm> <url>github.com/GedMarc/GuicedSwagger.git</url&gt; </scm> <dependencies> <dependency> <groupId>com.guicedee.servlets</groupId> <artifactId>guiced-rest-services</artifactId> <version>1.2.1.1-jre17</version> <scope>compile</scope>…

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Bioconductor – CeTF

DOI: 10.18129/B9.bioc.CeTF   Coexpression for Transcription Factors using Regulatory Impact Factors and Partial Correlation and Information Theory analysis Bioconductor version: Release (3.17) This package provides the necessary functions for performing the Partial Correlation coefficient with Information Theory (PCIT) (Reverter and Chan 2008) and Regulatory Impact Factors (RIF) (Reverter et al….

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Bioconductor – retrofit

DOI: 10.18129/B9.bioc.retrofit   RETROFIT: Reference-free deconvolution of cell mixtures in spatial transcriptomics Bioconductor version: Release (3.17) RETROFIT is a Bayesian non-negative matrix factorization framework to decompose cell type mixtures in ST data without using external single-cell expression references. RETROFIT outperforms existing reference-based methods in estimating cell type proportions and reconstructing…

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Microsoft Word – Abstract Book August 30, 2014

%PDF-1.6 % 1 0 obj <> endobj 27 0 obj <>/Font<>>>/Fields[]>> endobj 2 0 obj <>stream 2015-08-12T23:50:32-07:00 2015-08-12T23:50:32-07:00 2015-08-12T23:50:32-07:00 PScript5.dll Version 5.2.2 application/pdf Microsoft Word – Abstract Book August 30, 2014 welcome uuid:83621119-7315-422c-af8e-88300c668490 uuid:9a21fd37-e032-4073-926c-3a2dbebb702e GPL Ghostscript 8.15 endstream endobj 3 0 obj <> endobj 7 0 obj <>/Rotate 0/Type/Page>> endobj 26 0 obj <>stream x[r7+!v7[oa&@qin5))1ObO)9lE8JU@”x/7/ƁwG}mߎo/Oa”SƆQ.N9B9A38}wt!yz!,^XˣOR-\UEN&syQQ.+58i[ޯ2\ެ G#|%PTKrS#qx}Y$<[L>~.o#sVl00IUs b;%l lA8lL6u2sVV\=~’Y  Read more here: Source link

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Bioconductor – a4Classif

DOI: 10.18129/B9.bioc.a4Classif   Automated Affymetrix Array Analysis Classification Package Bioconductor version: Release (3.17) Functionalities for classification of Affymetrix microarray data, integrating within the Automated Affymetrix Array Analysis set of packages. Author: Willem Talloen [aut], Tobias Verbeke [aut], Laure Cougnaud [cre] Maintainer: Laure Cougnaud <laure.cougnaud at openanalytics.eu> Citation (from within R,…

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Bioconductor – CCPROMISE

DOI: 10.18129/B9.bioc.CCPROMISE   PROMISE analysis with Canonical Correlation for Two Forms of High Dimensional Genetic Data Bioconductor version: Release (3.17) Perform Canonical correlation between two forms of high demensional genetic data, and associate the first compoent of each form of data with a specific biologically interesting pattern of associations with…

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Bioconductor – granulator

DOI: 10.18129/B9.bioc.granulator   Rapid benchmarking of methods for *in silico* deconvolution of bulk RNA-seq data Bioconductor version: Release (3.17) granulator is an R package for the cell type deconvolution of heterogeneous tissues based on bulk RNA-seq data or single cell RNA-seq expression profiles. The package provides a unified testing interface…

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Bioconductor – ppcseq

DOI: 10.18129/B9.bioc.ppcseq   Probabilistic Outlier Identification for RNA Sequencing Generalized Linear Models Bioconductor version: Release (3.17) Relative transcript abundance has proven to be a valuable tool for understanding the function of genes in biological systems. For the differential analysis of transcript abundance using RNA sequencing data, the negative binomial model…

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Bioconductor – fcoex

DOI: 10.18129/B9.bioc.fcoex   FCBF-based Co-Expression Networks for Single Cells Bioconductor version: Release (3.17) The fcoex package implements an easy-to use interface to co-expression analysis based on the FCBF (Fast Correlation-Based Filter) algorithm. it was implemented especifically to deal with single-cell data. The modules found can be used to redefine cell…

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Bioconductor – POWSC

DOI: 10.18129/B9.bioc.POWSC   Simulation, power evaluation, and sample size recommendation for single cell RNA-seq Bioconductor version: Release (3.17) Determining the sample size for adequate power to detect statistical significance is a crucial step at the design stage for high-throughput experiments. Even though a number of methods and tools are available…

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Bioconductor – CiteFuse

DOI: 10.18129/B9.bioc.CiteFuse   CiteFuse: multi-modal analysis of CITE-seq data Bioconductor version: Release (3.17) CiteFuse pacakage implements a suite of methods and tools for CITE-seq data from pre-processing to integrative analytics, including doublet detection, network-based modality integration, cell type clustering, differential RNA and protein expression analysis, ADT evaluation, ligand-receptor interaction analysis,…

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Bioconductor – AlphaBeta

DOI: 10.18129/B9.bioc.AlphaBeta     This package is for version 3.11 of Bioconductor; for the stable, up-to-date release version, see AlphaBeta. Computational inference of epimutation rates and spectra from high-throughput DNA methylation data in plants Bioconductor version: 3.11 AlphaBeta is a computational method for estimating epimutation rates and spectra from high-throughput…

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Bioconductor – MACPET

DOI: 10.18129/B9.bioc.MACPET     This package is for version 3.15 of Bioconductor; for the stable, up-to-date release version, see MACPET. Model based analysis for paired-end data Bioconductor version: 3.15 The MACPET package can be used for complete interaction analysis for ChIA-PET data. MACPET reads ChIA-PET data in BAM or SAM…

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Bioconductor – ChIPsim

DOI: 10.18129/B9.bioc.ChIPsim     Simulation of ChIP-seq experiments Bioconductor version: Release (3.5) A general framework for the simulation of ChIP-seq data. Although currently focused on nucleosome positioning the package is designed to support different types of experiments. Author: Peter Humburg Maintainer: Peter Humburg <Peter.Humburg at gmail.com> Citation (from within R,…

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Bioconductor – maigesPack

DOI: 10.18129/B9.bioc.maigesPack     This package is for version 3.14 of Bioconductor; for the stable, up-to-date release version, see maigesPack. Functions to handle cDNA microarray data, including several methods of data analysis Bioconductor version: 3.14 This package uses functions of various other packages together with other functions in a coordinated…

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Bioconductor – SummarizedBenchmark

DOI: 10.18129/B9.bioc.SummarizedBenchmark   Classes and methods for performing benchmark comparisons Bioconductor version: Release (3.17) This package defines the BenchDesign and SummarizedBenchmark classes for building, executing, and evaluating benchmark experiments of computational methods. The SummarizedBenchmark class extends the RangedSummarizedExperiment object, and is designed to provide infrastructure to store and compare the…

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Enterprise generative AI: Take or shape?

Image source: 123RF “Take” “Take” refers to the traditional software-as-a-service (SaaS) model where you use the software “as is” off-the-shelf. There are various options available. They include: Public access: Access to closed tools like OpenAI’s ChatGPT may be viable for some organizations. It is also free (if you believe in…

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Bioconductor – ceRNAnetsim

DOI: 10.18129/B9.bioc.ceRNAnetsim     This package is for version 3.13 of Bioconductor; for the stable, up-to-date release version, see ceRNAnetsim. Regulation Simulator of Interaction between miRNA and Competing RNAs (ceRNA) Bioconductor version: 3.13 This package simulates regulations of ceRNA (Competing Endogenous) expression levels after a expression level change in one…

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Bioconductor – wavClusteR

DOI: 10.18129/B9.bioc.wavClusteR     This package is for version 3.12 of Bioconductor; for the stable, up-to-date release version, see wavClusteR. Sensitive and highly resolved identification of RNA-protein interaction sites in PAR-CLIP data Bioconductor version: 3.12 The package provides an integrated pipeline for the analysis of PAR-CLIP data. PAR-CLIP-induced transitions are…

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Bioconductor – GOpro

DOI: 10.18129/B9.bioc.GOpro     Find the most characteristic gene ontology terms for groups of human genes Bioconductor version: Release (3.14) Find the most characteristic gene ontology terms for groups of human genes. This package was created as a part of the thesis which was developed under the auspices of MI^2…

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Bioconductor – deepSNV

DOI: 10.18129/B9.bioc.deepSNV     This package is for version 3.15 of Bioconductor; for the stable, up-to-date release version, see deepSNV. Detection of subclonal SNVs in deep sequencing data. Bioconductor version: 3.15 This package provides provides quantitative variant callers for detecting subclonal mutations in ultra-deep (>=100x coverage) sequencing experiments. The deepSNV…

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Bioconductor – VariantExperiment

DOI: 10.18129/B9.bioc.VariantExperiment     This package is for version 3.12 of Bioconductor; for the stable, up-to-date release version, see VariantExperiment. A RangedSummarizedExperiment Container for VCF/GDS Data with GDS Backend Bioconductor version: 3.12 VariantExperiment is a Bioconductor package for saving data in VCF/GDS format into RangedSummarizedExperiment object. The high-throughput genetic/genomic data…

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Bioconductor – autonomics

DOI: 10.18129/B9.bioc.autonomics   Generifying and intuifying cross-platform omics analysis Bioconductor version: Release (3.17) This package offers a generic and intuitive solution for cross-platform omics data analysis. It has functions for import, preprocessing, exploration, contrast analysis and visualization of omics data. It follows a tidy, functional programming paradigm. Author: Aditya Bhagwat…

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Bioconductor – MsQuality

DOI: 10.18129/B9.bioc.MsQuality   MsQuality – Quality metric calculation from Spectra and MsExperiment objects Bioconductor version: Release (3.17) The MsQuality provides functionality to calculate quality metrics for mass spectrometry-derived, spectral data at the per-sample level. MsQuality relies on the mzQC framework of quality metrics defined by the Human Proteom Organization-Proteomics Standards…

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Bioconductor – rmspc

DOI: 10.18129/B9.bioc.rmspc   Multiple Sample Peak Calling Bioconductor version: Release (3.17) The rmspc package runs MSPC (Multiple Sample Peak Calling) software using R. The analysis of ChIP-seq samples outputs a number of enriched regions (commonly known as “peaks”), each indicating a protein-DNA interaction or a specific chromatin modification. When replicate…

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Open Source Mathematical Software (Free app)

SageMath is a free open-source mathematics software system licensed under the GPL. It builds on top of many existing open-source packages: NumPy, SciPy, matplotlib, Sympy, Maxima, GAP, FLINT, R and many more. Access their combined power through a common, Python-based language or directly via interfaces or wrappers. Mission Creating a…

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Bioconductor – SCArray.sat

DOI: 10.18129/B9.bioc.SCArray.sat   Large-scale single-cell RNA-seq data analysis using GDS files and Seurat Bioconductor version: Release (3.17) Extends the Seurat classes and functions to support Genomic Data Structure (GDS) files as a DelayedArray backend for data representation. It relies on the implementation of GDS-based DelayedMatrix in the SCArray package to…

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Problem installing Dependencies for R – JupyterHub

I am trying to set up an R env and install base packages for all users. The package lives on gitlab and I am using the following to install it. What happens is that during the deployment everything works fine and I can see this package being built and end…

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Bioconductor – DESeq

    This package is for version 2.10 of Bioconductor; for the stable, up-to-date release version, see DESeq. Differential gene expression analysis based on the negative binomial distribution Bioconductor version: 2.10 Estimate variance-mean dependence in count data from high-throughput sequencing assays and test for differential expression based on a model…

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Bioconductor – rrvgo

DOI: 10.18129/B9.bioc.rrvgo     Reduce + Visualize GO Bioconductor version: Release (3.13) Reduce and visualize lists of Gene Ontology terms by identifying redudance based on semantic similarity. Author: Sergi Sayols [aut, cre] Maintainer: Sergi Sayols <sergisayolspuig at gmail.com> Citation (from within R, enter citation(“rrvgo”)): Installation To install this package, start…

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Bioconductor – CATALYST

DOI: 10.18129/B9.bioc.CATALYST     This package is for version 3.12 of Bioconductor; for the stable, up-to-date release version, see CATALYST. Cytometry dATa anALYSis Tools Bioconductor version: 3.12 Mass cytometry (CyTOF) uses heavy metal isotopes rather than fluorescent tags as reporters to label antibodies, thereby substantially decreasing spectral overlap and allowing…

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Bioconductor – rnaSeqMap

DOI: 10.18129/B9.bioc.rnaSeqMap     This package is for version 3.12 of Bioconductor; for the stable, up-to-date release version, see rnaSeqMap. rnaSeq secondary analyses Bioconductor version: 3.12 The rnaSeqMap library provides classes and functions to analyze the RNA-sequencing data using the coverage profiles in multiple samples at a time Author: Anna…

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Bioconductor – chipenrich

DOI: 10.18129/B9.bioc.chipenrich     This package is for version 3.12 of Bioconductor; for the stable, up-to-date release version, see chipenrich. Gene Set Enrichment For ChIP-seq Peak Data Bioconductor version: 3.12 ChIP-Enrich and Poly-Enrich perform gene set enrichment testing using peaks called from a ChIP-seq experiment. The method empirically corrects for…

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Bioconductor – oppar

DOI: 10.18129/B9.bioc.oppar     Outlier profile and pathway analysis in R Bioconductor version: Release (3.5) The R implementation of mCOPA package published by Wang et al. (2012). Oppar provides methods for Cancer Outlier profile Analysis. Although initially developed to detect outlier genes in cancer studies, methods presented in oppar can…

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Bioconductor – esetVis

DOI: 10.18129/B9.bioc.esetVis     Visualizations of expressionSet Bioconductor object Bioconductor version: Release (3.5) Utility functions for visualization of expressionSet (or SummarizedExperiment) Bioconductor object, including spectral map, tsne and linear discriminant analysis. Static plot via the ggplot2 package or interactive via the ggvis or rbokeh packages are available. Author: Laure Cougnaud…

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Bioconductor – ENVISIONQuery

DOI: 10.18129/B9.bioc.ENVISIONQuery     This package is for version 3.13 of Bioconductor; for the stable, up-to-date release version, see ENVISIONQuery. Retrieval from the ENVISION bioinformatics data portal into R Bioconductor version: 3.13 Tools to retrieve data from ENVISION, the Database for Annotation, Visualization and Integrated Discovery portal Author: Alex Lisovich,…

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[PATCH] Add struct ad9832_platform_data to the include/linux/iio

[PATCH] Add struct ad9832_platform_data to the include/linux/iio * [PATCH] Add struct ad9832_platform_data to the include/linux/iio @ 2023-07-07 21:15 Madhumitha Prabakaran 2023-07-08 11:10 ` Greg Kroah-Hartman 0 siblings, 1 reply; 3+ messages in thread From: Madhumitha Prabakaran @ 2023-07-07 21:15 UTC (permalink / raw) To: Lars-Peter Clausen, Michael Hennerich, Jonathan Cameron,…

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Bioconductor – ISLET

DOI: 10.18129/B9.bioc.ISLET   Individual-Specific ceLl typE referencing Tool Bioconductor version: Release (3.17) ISLET is a method to conduct signal deconvolution for general -omics data. It can estimate the individual-specific and cell-type-specific reference panels, when there are multiple samples observed from each subject. It takes the input of the observed mixture…

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Bioconductor – txcutr

DOI: 10.18129/B9.bioc.txcutr   Transcriptome CUTteR Bioconductor version: Release (3.17) Various mRNA sequencing library preparation methods generate sequencing reads specifically from the transcript ends. Analyses that focus on quantification of isoform usage from such data can be aided by using truncated versions of transcriptome annotations, both at the alignment or pseudo-alignment…

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