Tag: testthat
Bioconductor – sSNAPPY (development version)
DOI: 10.18129/B9.bioc.sSNAPPY This is the development version of sSNAPPY; for the stable release version, see sSNAPPY. Single Sample directioNAl Pathway Perturbation analYsis Bioconductor version: Development (3.16) A single sample pathway pertrubation testing methods for RNA-seq data. The method propagate changes in gene expression down gene-set topologies to compute…
Bioconductor – ComplexHeatmap
DOI: 10.18129/B9.bioc.ComplexHeatmap This package is for version 3.14 of Bioconductor; for the stable, up-to-date release version, see ComplexHeatmap. Make Complex Heatmaps Bioconductor version: 3.14 Complex heatmaps are efficient to visualize associations between different sources of data sets and reveal potential patterns. Here the ComplexHeatmap package provides a highly…
Bioconductor – cytoKernel
DOI: 10.18129/B9.bioc.cytoKernel Differential expression using kernel-based score test Bioconductor version: Release (3.14) cytoKernel implements a kernel-based score test to identify differentially expressed features in high-dimensional biological experiments. This approach can be applied across many different high-dimensional biological data including gene expression data and dimensionally reduced cytometry-based marker expression…
Bioconductor – sccomp (development version)
DOI: 10.18129/B9.bioc.sccomp This is the development version of sccomp; to use it, please install the devel version of Bioconductor. Robust Outlier-aware Estimation of Composition and Heterogeneity for Single-cell Data Bioconductor version: Development (3.15) A robust and outlier-aware method for testing differential tissue composition from single-cell data. This model…
Bioconductor – GeuvadisTranscriptExpr
DOI: 10.18129/B9.bioc.GeuvadisTranscriptExpr This package is for version 3.8 of Bioconductor; for the stable, up-to-date release version, see GeuvadisTranscriptExpr. Data package with transcript expression and bi-allelic genotypes from the GEUVADIS project Bioconductor version: 3.8 Provides transcript expression and bi-allelic genotypes corresponding to the chromosome 19 for CEU individuals from…
Bioconductor – TAPseq
DOI: 10.18129/B9.bioc.TAPseq This package is for version 3.12 of Bioconductor; for the stable, up-to-date release version, see TAPseq. Targeted scRNA-seq primer design for TAP-seq Bioconductor version: 3.12 Design primers for targeted single-cell RNA-seq used by TAP-seq. Create sequence templates for target gene panels and design gene-specific primers using…
Bioconductor – adaptest
DOI: 10.18129/B9.bioc.adaptest This package is for version 3.11 of Bioconductor; for the stable, up-to-date release version, see adaptest. Data-Adaptive Statistics for High-Dimensional Multiple Testing Bioconductor version: 3.11 Data-adaptive test statistics represent a general methodology for performing multiple hypothesis testing on effects sizes while maintaining honest statistical inference when…
Bioconductor – OGRE (development version)
DOI: 10.18129/B9.bioc.OGRE This is the development version of OGRE; to use it, please install the devel version of Bioconductor. Calculate, visualize and analyse overlap between genomic regions Bioconductor version: Development (3.15) OGRE calculates overlap between user defined genomic region datasets. Any regions can be supplied i.e. genes, SNPs,…
Bioconductor – txcutr (development version)
DOI: 10.18129/B9.bioc.txcutr This is the development version of txcutr; for the stable release version, see txcutr. Transcriptome CUTteR Bioconductor version: Development (3.15) 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…
Bioconductor – DaMiRseq (development version)
DOI: 10.18129/B9.bioc.DaMiRseq This is the development version of DaMiRseq; for the stable release version, see DaMiRseq. Data Mining for RNA-seq data: normalization, feature selection and classification Bioconductor version: Development (3.15) The DaMiRseq package offers a tidy pipeline of data mining procedures to identify transcriptional biomarkers and exploit them…
Bioconductor – RiboCrypt
DOI: 10.18129/B9.bioc.RiboCrypt Interactive visualization in genomics Bioconductor version: Release (3.14) R Package for interactive visualization and browsing NGS data. It contains a browser for both transcript and genomic coordinate view. In addition a QC and general metaplots are included, among others differential translation plots and gene expression plots….
Bioconductor – derfinder (development version)
DOI: 10.18129/B9.bioc.derfinder This is the development version of derfinder; for the stable release version, see derfinder. Annotation-agnostic differential expression analysis of RNA-seq data at base-pair resolution via the DER Finder approach Bioconductor version: Development (3.15) This package provides functions for annotation-agnostic differential expression analysis of RNA-seq data. Two…
Bioconductor – TBSignatureProfiler (development version)
DOI: 10.18129/B9.bioc.TBSignatureProfiler This is the development version of TBSignatureProfiler; for the stable release version, see TBSignatureProfiler. Profile RNA-Seq Data Using TB Pathway Signatures Bioconductor version: Development (3.15) Gene signatures of TB progression, TB disease, and other TB disease states have been validated and published previously. This package aggregates…
Bioconductor – easierData
DOI: 10.18129/B9.bioc.easierData easier internal data and exemplary dataset from IMvigor210CoreBiologies package Bioconductor version: Release (3.14) Access to internal data required for the functional performance of easier package and exemplary bladder cancer dataset with both processed RNA-seq data and information on response to ICB therapy generated by Mariathasan et…
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…
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…
Description, Programming Languages, Similar Projects of Rbert
RBERT is an R implementation of the Python package BERT developed at Google for Natural Language Processing. Installation You can install RBERT from GitHub with: # install.packages(“devtools”) devtools::install_github( “jonathanbratt/RBERT”, build_vignettes = TRUE ) TensorFlow Installation RBERT requires TensorFlow. Currently the version must be <= 1.13.1. You can install it using…
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…
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…
Bioconductor – PAIRADISE
DOI: 10.18129/B9.bioc.PAIRADISE This package is for version 3.9 of Bioconductor; for the stable, up-to-date release version, see PAIRADISE. PAIRADISE: Paired analysis of differential isoform expression Bioconductor version: 3.9 This package implements the PAIRADISE procedure for detecting differential isoform expression between matched replicates in paired RNA-Seq data. Author: Levon…
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…
Bioconductor – ALDEx2
DOI: 10.18129/B9.bioc.ALDEx2 This package is for version 3.9 of Bioconductor; for the stable, up-to-date release version, see ALDEx2. Analysis Of Differential Abundance Taking Sample Variation Into Account Bioconductor version: 3.9 A differential abundance analysis for the comparison of two or more conditions. Useful for analyzing data from standard…
Bioconductor – TBSignatureProfiler
DOI: 10.18129/B9.bioc.TBSignatureProfiler This package is for version 3.12 of Bioconductor; for the stable, up-to-date release version, see TBSignatureProfiler. Profile RA-Seq Data Using TB Pathway Signatures Bioconductor version: 3.12 Signatures of TB progression, TB disease, and other TB disease states have been created. This package makes it easy to…
Accepted r-bioc-deseq2 1.32.0+dfsg-1 (source) into unstable
—–BEGIN PGP SIGNED MESSAGE—– Hash: SHA512 Format: 1.8 Date: Tue, 14 Sep 2021 00:18:17 +0530 Source: r-bioc-deseq2 Architecture: source Version: 1.32.0+dfsg-1 Distribution: unstable Urgency: medium Maintainer: Debian R Packages Maintainers <r-pkg-t…@alioth-lists.debian.net> Changed-By: Nilesh Patra <nil…@debian.org> Changes: r-bioc-deseq2 (1.32.0+dfsg-1) unstable; urgency=medium . [ Andreas Tille ] * Team Upload. * New…
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…
Bioconductor – RNAmodR.Data
DOI: 10.18129/B9.bioc.RNAmodR.Data Example data for the RNAmodR package Bioconductor version: Release (3.13) RNAmodR.Data contains example data, which is used for vignettes and example workflows in the RNAmodR and dependent packages. Author: Felix G.M. Ernst [aut, cre], Denis L.J. Lafontaine [ctb, fnd] Maintainer: Felix G.M. Ernst <felix.gm.ernst at outlook.com>…
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…
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…
Bioconductor – MetaGxPancreas
DOI: 10.18129/B9.bioc.MetaGxPancreas This package is for version 3.10 of Bioconductor; for the stable, up-to-date release version, see MetaGxPancreas. Transcriptomic Pancreatic Cancer Datasets Bioconductor version: 3.10 A collection of pancreatic Cancer transcriptomic datasets that are part of the MetaGxData package compendium. Author: Michael Zon <michaelzon7 at gmail.com>, Vandana Sandhu…
Bioconductor – ttgsea (development version)
DOI: 10.18129/B9.bioc.ttgsea This is the development version of ttgsea; for the stable release version, see ttgsea. Tokenizing Text of Gene Set Enrichment Analysis Bioconductor version: Development (3.14) Functional enrichment analysis methods such as gene set enrichment analysis (GSEA) have been widely used for analyzing gene expression data. GSEA…
Bioconductor – traviz (development version)
DOI: 10.18129/B9.bioc.traviz This is the development version of traviz; to use it, please install the devel version of Bioconductor. Trajectory functions for visualization and interpretation. Bioconductor version: Development (3.14) traviz provides a suite of functions to plot trajectory related objects from Bioconductor packages. It allows plotting trajectories in…
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…
Bioconductor – ReactomeContentService4R (development version)
DOI: 10.18129/B9.bioc.ReactomeContentService4R This is the development version of ReactomeContentService4R; for the stable release version, see ReactomeContentService4R. Interface for the Reactome Content Service Bioconductor version: Development (3.14) Reactome is a free, open-source, open access, curated and peer-reviewed knowledgebase of bio-molecular pathways. This package is to interact with the Reactome…
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…
List of all packages in BioConductor transition dependency level 1 failing due issue with either RUnit or testthat)
Hi, thanks to several hints I was able to nearly solve all issues. On Thu, Sep 02, 2021 at 01:12:29PM +0200, Andreas Tille wrote: > > The packages in question are mentioned as Test-Depends and I have no > idea why these are not found. It was solved by accorcing…
List of all packages in BioConductor transition dependency level 1 failing due issue with either RUnit or testthat
Hi Andreas, On 02-09-2021 13:12, Andreas Tille wrote: > I did added an info about all those packages of level 1 that are failing > either due to RUnit or testthat issues and here is a manually edited > `grep -A8 ‘/jobs/’ r-bioc-*/debian/changelog` on my local disk: > > r-bioc-biocparallel/debian/changelog:…
Bioconductor – scRNAseq
DOI: 10.18129/B9.bioc.scRNAseq This package is for version 3.11 of Bioconductor; for the stable, up-to-date release version, see scRNAseq. Collection of Public Single-Cell RNA-Seq Datasets Bioconductor version: 3.11 Gene-level counts for a collection of public scRNA-seq datasets, provided as SingleCellExperiment objects with cell- and gene-level metadata. Author: Davide Risso…
Bioconductor – DESeq2
DOI: 10.18129/B9.bioc.DESeq2 This package is for version 3.10 of Bioconductor; for the stable, up-to-date release version, see DESeq2. Differential gene expression analysis based on the negative binomial distribution Bioconductor version: 3.10 Estimate variance-mean dependence in count data from high-throughput sequencing assays and test for differential expression based on…
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…