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Package Name Access Summary Updated
snakemake-minimal public A popular workflow management system aiming at full in-silico reproducibility. 2024-11-05
perl-class-xsaccessor public Generate fast XS accessors without runtime compilation 2024-11-05
perl-indirect public Lexically warn about using the indirect method call syntax. 2024-11-05
perl-time-hires public High resolution alarm, sleep, gettimeofday, interval timers 2024-11-05
perl-unicode-utf8 public Encoding and decoding of UTF-8 encoding form 2024-11-05
perl-list-moreutils-xs public Provide the stuff missing in List::Util in XS 2024-10-31
pbmm2 public A minimap2 frontend for PacBio native data formats 2024-10-29
altamisa public Alternative Python API for accessing ISA-tab files. 2024-10-28
lofreq public A fast and sensitive variant-caller for inferring SNVs and indels from next-generation sequencing data 2024-10-26
snippy public Rapid bacterial SNP calling and core genome alignments 2024-10-24
snakedeploy public Helper for deploying published Snakemake pipelines. 2024-10-23
busco public Assessment of assembly completeness using Universal Single Copy Orthologs. 2024-10-11
gtotree public GToTree is a user-friendly workflow for phylogenomics. 2024-10-07
trnascan-se public tRNA detection in large-scale genomic sequences 2024-09-27
mummer public MUMmer is a system for rapidly aligning entire genomes 2024-09-13
bcftools public BCFtools is a set of utilities that manipulate variant calls in the Variant Call Format (VCF) and its binary counterpart BCF. All commands work transparently with both VCFs and BCFs, both uncompressed and BGZF-compressed. Most commands accept VCF, bgzipped VCF and BCF with filetype detected automatically even when streaming from a pipe. Indexed VCF and BCF will work in all situations. Un-indexed VCF and BCF and streams will work in most, but not all situations. 2024-09-12
htslib public C library for high-throughput sequencing data formats. 2024-09-12
freebayes public Bayesian haplotype-based polymorphism discovery and genotyping 2024-09-10
bowtie2 public A fast and sensitive gapped read aligner. 2024-08-21
treetime public Maximum-Likelihood dating and ancestral inference for phylogenetic trees 2024-08-11
umi_tools public Tools for dealing with Unique Molecular Identifiers (UMIs) / Random Molecular Tags (RMTs) 2024-08-05
trinity public Trinity assembles transcript sequences from Illumina RNA-Seq data. 2024-08-04
bracken public Bracken (Bayesian Reestimation of Abundance with KrakEN) is a highly accurate statistical method that computes the abundance of species in DNA sequences from a metagenomics sample. 2024-07-22
gffcompare public GffCompare by Geo Pertea 2024-07-18
bamtools public C++ API & command-line toolkit for working with BAM data 2024-07-10
hicexplorer public Set of programs to process, analyze and visualize Hi-C and capture Hi-C data 2024-06-28
genomelake public Simple and efficient random access to genomic data for deep learning models. 2024-06-12
genometools-genometools public GenomeTools genome analysis system. 2024-06-12
peakachu public Peak calling tool for CLIP-seq data. 2024-06-11
htseq public HTSeq is a Python library to facilitate processing and analysis of data from high-throughput sequencing (HTS) experiments. 2024-06-11
libmaus2 public collection of data structures and algorithms for NGS data 2024-06-08
bioconductor-deseq2 public Differential gene expression analysis based on the negative binomial distribution 2024-05-30
bioconductor-rtracklayer public R interface to genome annotation files and the UCSC genome browser 2024-05-27
bioconductor-hdf5array public HDF5 backend for DelayedArray objects 2024-05-10
bioconductor-rhdf5 public R Interface to HDF5 2024-05-10
bioconductor-mzr public parser for netCDF, mzXML, mzData and mzML and mzIdentML files (mass spectrometry data) 2024-05-09
stringtie public StringTie employs efficient algorithms for transcript structure recovery and abundance estimation from bulk RNA-Seq reads aligned to a reference genome. 2024-05-08
bioconductor-genomicranges public Representation and manipulation of genomic intervals 2024-05-06
bioconductor-rhdf5lib public hdf5 library as an R package 2024-05-06
bioconductor-iranges public Foundation of integer range manipulation in Bioconductor 2024-05-02
bioconductor-xvector public Foundation of external vector representation and manipulation in Bioconductor 2024-05-02
bioconductor-s4vectors public Foundation of vector-like and list-like containers in Bioconductor 2024-05-01
bioconductor-dexseq public Inference of differential exon usage in RNA-Seq 2024-04-02
deeptools public A set of user-friendly tools for normalization and visualzation of deep-sequencing data 2024-03-08
scanpy-scripts public Scripts for using scanpy from the command line 2024-02-21
raptor public Raptor: A fast and space-efficient pre-filter for querying very large collections of nucleotide sequences 2024-01-17
bioconductor-genomeinfodb public Utilities for manipulating chromosome names, including modifying them to follow a particular naming style 2023-12-06
bioconductor-genomeinfodbdata public Species and taxonomy ID look up tables used by GenomeInfoDb 2023-12-05
bioconductor-data-packages public A package to enable downloading and installation of Bioconductor data packages 2023-12-04
bioconductor-biocgenerics public S4 generic functions used in Bioconductor 2023-12-04

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