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Package Name Access Summary Updated
rsem public RSEM is a software package for estimating gene and isoform expression levels from RNA-Seq data. 2024-12-16
bamcmp public Tools for deconvolving host and graft reads using full-length alignments and their scores. 2024-12-16
dna-nn public Model and predict short DNA sequence features with neural networks. 2024-12-16
pasa public PASA, acronym for Program to Assemble Spliced Alignments (and pronounced 'pass-uh'), is a eukaryotic genome annotation tool that exploits spliced alignments of expressed transcript sequences to automatically model gene structures, and to maintain gene structure annotation consistent with the most recently available experimental sequence data. PASA also identifies and classifies all splicing variations supported by the transcript alignments. 2024-12-16
nextpolish2 public Repeat-aware polishing genomes assembled using HiFi long reads. 2024-12-16
namfinder public Finds Non-overlapping Approximate Matches (NAMs) between query and reference sequences using strobemers 2024-12-16
bioconductor-rhdf5lib public hdf5 library as an R package 2024-12-16
seshat public Tools for programmatically annotating VCFs with the Seshat TP53 database. 2024-12-16
sentieon public Accelerated performance bioinformatics tools for mapping and variant calling 2024-12-16
sylph public sylph quickly enables querying of genomes against even low-coverage shotgun metagenomes to find nearest neighbour ANI. 2024-12-16
ms-entropy public This package provides a Python implementation of calculating spectral entropy, entropy similarity, and Flash entropy search for mass spectrometry data. 2024-12-16
purge_dups public Purge_dups is a package used to purge haplotigs and overlaps in an assembly based on read depth 2024-12-16
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
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