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Package Name Access Summary Updated
perl-escape-houdini public Perl API to Houdini, a zero-dependency C web escaping library 2024-12-16
perl-config-autoconf public A module to implement some of AutoConf macros in pure perl. 2024-12-16
bioconductor-timecourse public Statistical Analysis for Developmental Microarray Time Course Data 2024-12-16
methyldackel public A (mostly) universal methylation extractor for BS-seq experiments. Formerly named PileOMeth. 2024-12-16
libsequence public A C++ class library for evolutionary genetics. 2024-12-16
meme public Motif-based sequence analysis tools. 2024-12-16
pycluster public Clustering module for Python 2024-12-16
pindel public Pindel can detect breakpoints of large deletions, medium sized insertions, inversions, tandem duplications and other structural variants at single-based resolution from next-gen sequence data 2024-12-16
bioconductor-rnaseqcovarimpute public Impute Covariate Data in RNA Sequencing Studies 2024-12-16
bioconductor-cytolib public C++ infrastructure for representing and interacting with the gated cytometry data 2024-12-16
perl-sanger-cgp-allelecount public Support code for NGS copy number algorithm 2024-12-16
perl-datetime-locale public Localization support for DateTime.pm 2024-12-16
msisensor-pro public Microsatellite Instability (MSI) detection using high-throughput sequencing data. 2024-12-16
alfred public BAM alignment statistics, feature counting and feature annotation 2024-12-16
trnascan-se public tRNA detection in large-scale genomic sequences 2024-12-16
phispy public Prophage finder using multiple metrics 2024-12-16
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
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
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