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Package Name Access Summary Updated
bioconductor-reactomegsa public Client for the Reactome Analysis Service for comparative multi-omics gene set analysis 2024-12-16
cvlr public Clustering and Visualization of Long Reads 2024-12-16
bioconductor-biodist public Different distance measures 2024-12-16
ngslca public ngsLCA: fast and flexible taxonomic classification of DNA reads aligned to reference databases 2024-12-16
r-mgsz public Performs gene set analysis based on GSZ scoring function and asymptotic p-value. It is different from GSZ in that it implements asymptotic p-values instead of empirical p-values. Asymptotic p-values are calculated by fitting suitable distribution model to the null distribution. Unlike empirical p-values, resolution of asymptotic p-values are independent of the number of permutations and hence requires considerably fewer permutations. In addition, this package allows gene set analysis with seven other popular gene set analysis methods. 2024-12-16
vcfdist public vcfdist: benchmarking phased germline variant calls in VCF format 2024-12-16
leviosam public lift-over of alignments for variant-aware references 2024-12-16
hecatomb public Hecatomb: and end-to-end platform for viral metagenomics 2024-12-16
mashpit public Sketch-based surveillance platform. 2024-12-16
bioconductor-progeny public Pathway RespOnsive GENes for activity inference from gene expression 2024-12-16
ataqv public ataqv is a toolkit for measuring and comparing ATAC-seq results. It was written to help understand how well ATAC-seq assays have worked, and to make it easier to spot differences that might be caused by library prep or sequencing. 2024-12-16
bioconductor-plpe public Local Pooled Error Test for Differential Expression with Paired High-throughput Data 2024-12-16
bioconductor-bayesknockdown public BayesKnockdown: Posterior Probabilities for Edges from Knockdown Data 2024-12-16
methpipe public A pipeline for analyzing DNA methylation data from bisulfite sequencing. 2024-12-16
bioconductor-river public R package for RIVER (RNA-Informed Variant Effect on Regulation) 2024-12-16
samtools public Tools for dealing with SAM, BAM and CRAM files 2024-12-16
bioconductor-mipp public Misclassification Penalized Posterior Classification 2024-12-16
bioconductor-a4preproc public Automated Affymetrix Array Analysis Preprocessing Package 2024-12-16
bioconductor-mfuzz public Soft clustering of omics time series data 2024-12-16
bioconductor-lapmix public Laplace Mixture Model in Microarray Experiments 2024-12-16
viral_consensus public Fast viral consensus genome reconstruction 2024-12-16
bioconductor-rbsurv public Robust likelihood-based survival modeling with microarray data 2024-12-16
ksnp public k-mer based haplotype assembly 2024-12-16
r-classdiscovery public Defines the classes used for "class discovery" problems in the OOMPA project (<http://oompa.r-forge.r-project.org/>). Class discovery primarily consists of unsupervised clustering methods with attempts to assess their statistical significance. 2024-12-16
dnmtools public dnmtools is a set of tools for analyzing DNA methylation data from bisulfite sequencing. 2024-12-16
bioconductor-hybridmtest public Hybrid Multiple Testing 2024-12-16
gencore public Generate consensus reads to reduce sequencing noises and remove duplications 2024-12-16
r-music public Companion package to: A bulk tissue deconvolution method with multi-subject single cell expression reference. This package provide functions to estimate bulk tissue cell type proportions with multi-subject single cell expression as reference. 2024-12-16
bioconductor-gwastools public Tools for Genome Wide Association Studies 2024-12-16
preseq public predicting library complexity and genome coverage in high-throughput sequencing 2024-12-16
bioconductor-rtpca public Thermal proximity co-aggregation with R 2024-12-16
bioconductor-aims public AIMS : Absolute Assignment of Breast Cancer Intrinsic Molecular Subtype 2024-12-16
psirc public Full-length linear and circular transcript isoform reconstruction and quantification. 2024-12-16
bioconductor-nanotube public An Easy Pipeline for NanoString nCounter Data Analysis 2024-12-16
wally public Visualization of aligned sequencing reads and genomic variants. 2024-12-16
bioconductor-roastgsa public Rotation based gene set analysis 2024-12-16
bioconductor-clippda public A package for the clinical proteomic profiling data analysis 2024-12-16
r-aroma.core public Core methods and classes used by higher-level 'aroma.*' packages part of the Aroma Project, e.g. 'aroma.affymetrix' and 'aroma.cn'. 2024-12-16
smartmap public SmartMap: Bayesian Analysis of Ambiguously Mapped Reads 2024-12-16
bioconductor-cbpmanager public Generate, manage, and edit data and metadata files suitable for the import in cBioPortal for Cancer Genomics 2024-12-16
bioconductor-hca public Exploring the Human Cell Atlas Data Coordinating Platform 2024-12-16
bioconductor-snifter public R wrapper for the python openTSNE library 2024-12-16
bioconductor-ihw public Independent Hypothesis Weighting 2024-12-16
fastq-filter public A fast FASTQ filter program. 2024-12-16
bpp-phyl public Bio++ is a set of C++ libraries for Bioinformatics. 2024-12-16
ultraplex public fastq demultiplexer 2024-12-16
cutadapt public Trim adapters from high-throughput sequencing reads 2024-12-16
viewbs public ViewBS is a powerful toolkit for visualization of high-throughput bisulfite sequencing data 2024-12-16
bioconductor-interactivedisplaybase public Base package for enabling powerful shiny web displays of Bioconductor objects 2024-12-16
bpp-popgen public Bio++ is a set of C++ libraries for Bioinformatics. 2024-12-16
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