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Package Name Access Summary Updated
edta public Extensive de-novo TE Annotator 2024-12-16
bioconductor-iterativebma public The Iterative Bayesian Model Averaging (BMA) algorithm 2024-12-16
bioconductor-generecommender public A gene recommender algorithm to identify genes coexpressed with a query set of genes 2024-12-16
paf2chain public convert PAF format to CHAIN format 2024-12-16
bioconductor-subseq public Subsampling of high-throughput sequencing count data 2024-12-16
softsv public SoftSV is a tool for the detection of small and large deletions, inversions, tandem duplications and translocations from paired-end sequencing data. 2024-12-16
bioconductor-geneclassifiers public Application of gene classifiers 2024-12-16
bioconductor-rols public An R interface to the Ontology Lookup Service 2024-12-16
bioconductor-specond public Condition specific detection from expression data 2024-12-16
megadepth public Megadepth is an efficient tool for extracting coverage related information from RNA and DNA-seq BAM and BigWig files. It supports reading whole-genome coverage from BAM files and writing either indexed TSV or BigWig files, as well as efficient region coverage summary over intervals from both types of files. 2024-12-16
bioconductor-pandar public PANDA Algorithm 2024-12-16
wiggletools public The WiggleTools package allows genomewide data files to be manipulated as numerical functions, equipped with all the standard functional analysis operators (sum, product, product by a scalar, comparators), and derived statistics (mean, median, variance, stddev, t-test, Wilcoxon's rank sum test, etc). 2024-12-16
bioconductor-coveb public Empirical Bayes estimate of block diagonal covariance matrices 2024-12-16
superstr public A lightweight, alignment-free utility for detecting repeat-containing reads in short-read WGS, WES and RNA-seq data. 2024-12-16
bioconductor-rmagpie public MicroArray Gene-expression-based Program In Error rate estimation 2024-12-16
cyvcf2 public A cython wrapper around htslib built for fast parsing of Variant Call Format (VCF) files 2024-12-16
bioconductor-a4core public Automated Affymetrix Array Analysis Core Package 2024-12-16
expansionhunter public A tool for estimating repeat sizes 2024-12-16
bioconductor-normalize450k public Preprocessing of Illumina Infinium 450K data 2024-12-16
bioconductor-ecolitk public Meta-data and tools for E. coli 2024-12-16
dicey public In-silico PCR and variant primer design 2024-12-16
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
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