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Package Name Access Summary Updated
r-cate public Provides several methods for factor analysis in high dimension (both n,p >> 1) and methods to adjust for possible confounders in multiple hypothesis testing. 2025-01-01
bioconductor-motifstack public Plot stacked logos for single or multiple DNA, RNA and amino acid sequence 2024-12-31
bioconductor-chromvar public Chromatin Variation Across Regions 2024-12-31
r-deconstructsigs public Takes sample information in the form of the fraction of mutations in each of 96 trinucleotide contexts and identifies the weighted combination of published signatures that, when summed, most closely reconstructs the mutational profile. 2024-12-31
bioconductor-chipcomp public Quantitative comparison of multiple ChIP-seq datasets 2024-12-31
bioconductor-codex public A Normalization and Copy Number Variation Detection Method for Whole Exome Sequencing 2024-12-31
bioconductor-madseq public Mosaic Aneuploidy Detection and Quantification using Massive Parallel Sequencing Data 2024-12-31
bioconductor-traser public GWAS trait-associated SNP enrichment analyses in genomic intervals 2024-12-31
bioconductor-fccac public functional Canonical Correlation Analysis to evaluate Covariance between nucleic acid sequencing datasets 2024-12-31
bioconductor-cexor public An R package to uncover high-resolution protein-DNA interactions in ChIP-exo replicates 2024-12-31
bioconductor-snphood public SNPhood: Investigate, quantify and visualise the epigenomic neighbourhood of SNPs using NGS data 2024-12-31
bioconductor-varianttools public Tools for Exploratory Analysis of Variant Calls 2024-12-31
bioconductor-dss public Dispersion shrinkage for sequencing data 2024-12-31
bioconductor-bsseq public Analyze, manage and store whole-genome methylation data 2024-12-31
bioconductor-mutationalpatterns public Comprehensive genome-wide analysis of mutational processes 2024-12-31
bioconductor-titancna public Subclonal copy number and LOH prediction from whole genome sequencing of tumours 2024-12-31
bioconductor-myvariant public Accesses MyVariant.info variant query and annotation services 2024-12-31
bioconductor-bbcanalyzer public BBCAnalyzer: an R/Bioconductor package for visualizing base counts 2024-12-31
bioconductor-uniquorn public Identification of cancer cell lines based on their weighted mutational/ variational fingerprint 2024-12-31
bioconductor-purecn public Copy number calling and SNV classification using targeted short read sequencing 2024-12-31
bioconductor-genomicfiles public Distributed computing by file or by range 2024-12-31
bioconductor-helloranges public Introduce *Ranges to bedtools users 2024-12-31
bioconductor-basic4cseq public Basic4Cseq: an R/Bioconductor package for analyzing 4C-seq data 2024-12-31
bioconductor-vanillaice public A Hidden Markov Model for high throughput genotyping arrays 2024-12-31
bioconductor-tfbstools public Software Package for Transcription Factor Binding Site (TFBS) Analysis 2024-12-31
bioconductor-hdf5array public HDF5 datasets as array-like objects in R 2024-12-31
bioconductor-cleanupdtseq public cleanUpdTSeq cleans up artifacts from polyadenylation sites from oligo(dT)-mediated 3' end RNA sequending data 2024-12-31
bioconductor-ensdb.hsapiens.v75 public Exposes an annotation databases generated from Ensembl. 2024-12-31
bioconductor-scrnaseq public Collection of Public Single-Cell RNA-Seq Datasets 2024-12-31
bioconductor-ruvseq public Remove Unwanted Variation from RNA-Seq Data 2024-12-31
bioconductor-minfi public Analyze Illumina Infinium DNA methylation arrays 2024-12-31
bioconductor-affycoretools public Functions useful for those doing repetitive analyses with Affymetrix GeneChips 2024-12-31
bioconductor-reportingtools public Tools for making reports in various formats 2024-12-31
bioconductor-chipseq public chipseq: A package for analyzing chipseq data 2024-12-30
bioconductor-girafe public Genome Intervals and Read Alignments for Functional Exploration 2024-12-30
bioconductor-cner public CNE Detection and Visualization 2024-12-30
bioconductor-shortread public FASTQ input and manipulation 2024-12-30
bioconductor-rhdf5 public R Interface to HDF5 2024-12-30
bioconductor-inspect public Modeling RNA synthesis, processing and degradation with RNA-seq data 2024-12-30
bioconductor-imas public Integrative analysis of Multi-omics data for Alternative Splicing 2024-12-30
bioconductor-rtcgatoolbox public A new tool for exporting TCGA Firehose data 2024-12-30
bioconductor-rgreat public GREAT Analysis - Functional Enrichment on Genomic Regions 2024-12-30
bioconductor-rcgh public Comprehensive Pipeline for Analyzing and Visualizing Array-Based CGH Data 2024-12-30
bioconductor-fdb.infiniummethylation.hg19 public Compiled HumanMethylation27 and HumanMethylation450 annotations 2024-12-30
bioconductor-proloc public A unifying bioinformatics framework for spatial proteomics 2024-12-30
bioconductor-gostats public Tools for manipulating GO and microarrays 2024-12-30
bioconductor-doppelgangr public Identify likely duplicate samples from genomic or meta-data 2024-12-30
bioconductor-trigger public Transcriptional Regulatory Inference from Genetics of Gene ExpRession 2024-12-30
bioconductor-ballgown public Flexible, isoform-level differential expression analysis 2024-12-30
r-leapp public These functions take a gene expression value matrix, a primary covariate vector, an additional known covariates matrix. A two stage analysis is applied to counter the effects of latent variables on the rankings of hypotheses. The estimation and adjustment of latent effects are proposed by Sun, Zhang and Owen (2011). "leapp" is developed in the context of microarray experiments, but may be used as a general tool for high throughput data sets where dependence may be involved. 2024-12-30
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