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snakemake-minimal
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public |
A popular workflow management system aiming at full in-silico reproducibility.
|
2025-01-08 |
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stringtie
|
public |
StringTie employs efficient algorithms for transcript structure recovery and abundance estimation from bulk RNA-Seq reads aligned to a reference genome.
|
2025-01-07 |
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bioconductor-data-packages
|
public |
A package to enable downloading and installation of Bioconductor data packages
|
2025-01-05 |
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bioconductor-hdf5array
|
public |
HDF5 datasets as array-like objects in R
|
2024-12-31 |
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bioconductor-rhdf5
|
public |
R Interface to HDF5
|
2024-12-30 |
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ngscheckmate
|
public |
Software package for identifying next generation sequencing (NGS) data files from the same individual.
|
2024-12-28 |
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bioconductor-rtracklayer
|
public |
R interface to genome annotation files and the UCSC genome browser
|
2024-12-27 |
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bioconductor-deseq2
|
public |
Differential gene expression analysis based on the negative binomial distribution
|
2024-12-27 |
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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.
|
2024-12-27 |
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trinity
|
public |
Trinity assembles transcript sequences from Illumina RNA-Seq data.
|
2024-12-26 |
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bioconductor-dexseq
|
public |
Inference of differential exon usage in RNA-Seq
|
2024-12-25 |
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r-sceasy
|
public |
A package providing functions to convert between different single-cell data formats.
|
2024-12-25 |
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perl-datetime
|
public |
A date and time object for Perl
|
2024-12-19 |
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bioconductor-genomicranges
|
public |
Representation and manipulation of genomic intervals
|
2024-12-19 |
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htseq
|
public |
HTSeq is a Python library to facilitate processing and analysis of data from high-throughput sequencing (HTS) experiments.
|
2024-12-19 |
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bioconductor-xvector
|
public |
Foundation of external vector representation and manipulation in Bioconductor
|
2024-12-19 |
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umi_tools
|
public |
Tools for dealing with Unique Molecular Identifiers (UMIs) / Random Molecular Tags (RMTs).
|
2024-12-19 |
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bioconductor-genomeinfodb
|
public |
Utilities for manipulating chromosome names, including modifying them to follow a particular naming style
|
2024-12-18 |
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perl-list-moreutils-xs
|
public |
Provide the stuff missing in List::Util in XS
|
2024-12-18 |
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bioconductor-mzr
|
public |
parser for netCDF, mzXML and mzML and mzIdentML files (mass spectrometry data)
|
2024-12-18 |
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bioconductor-iranges
|
public |
Foundation of integer range manipulation in Bioconductor
|
2024-12-18 |
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lofreq
|
public |
A fast and sensitive variant-caller for inferring SNVs and indels from next-generation sequencing data
|
2024-12-17 |
|
bioconductor-genomeinfodbdata
|
public |
Species and taxonomy ID look up tables used by GenomeInfoDb
|
2024-12-17 |
|
bioconductor-s4vectors
|
public |
Foundation of vector-like and list-like containers in Bioconductor
|
2024-12-17 |
|
perl-sub-attribute
|
public |
Reliable subroutine attribute handlers
|
2024-12-16 |
|
trnascan-se
|
public |
tRNA detection in large-scale genomic sequences
|
2024-12-16 |
|
bioconductor-rhdf5lib
|
public |
hdf5 library as an R package
|
2024-12-16 |
|
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.
|
2024-12-15 |
|
perl-html-parser
|
public |
HTML parser class
|
2024-12-15 |
|
perl-class-xsaccessor
|
public |
Generate fast XS accessors without runtime compilation
|
2024-12-15 |
|
libmaus2
|
public |
Collection of data structures and algorithms for NGS data.
|
2024-12-14 |
|
perl-params-validate
|
public |
Validate method/function parameters
|
2024-12-14 |
|
bioconductor-biocgenerics
|
public |
S4 generic functions used in Bioconductor
|
2024-12-14 |
|
perl-indirect
|
public |
Lexically warn about using the indirect method call syntax.
|
2024-12-14 |
|
htslib
|
public |
C library for high-throughput sequencing data formats.
|
2024-12-14 |
|
perl-time-hires
|
public |
High resolution alarm, sleep, gettimeofday, interval timers
|
2024-12-14 |
|
mummer
|
public |
MUMmer is a system for rapidly aligning entire genomes
|
2024-12-13 |
|
pbmm2
|
public |
A minimap2 frontend for PacBio native data formats
|
2024-12-13 |
|
pizzly
|
public |
Fast fusion detection using kallisto
|
2024-12-13 |
|
perl-unicode-utf8
|
public |
Encoding and decoding of UTF-8 encoding form
|
2024-12-13 |
|
bamtools
|
public |
C++ API & command-line toolkit for working with BAM data
|
2024-12-13 |
|
raptor
|
public |
Raptor: A fast and space-efficient pre-filter for querying very large collections of nucleotide sequences
|
2024-12-12 |
|
gffcompare
|
public |
GffCompare by Geo Pertea
|
2024-12-12 |
|
bowtie2
|
public |
A fast and sensitive gapped read aligner.
|
2024-12-12 |
|
mentalist
|
public |
The MLST pipeline developed by the PathOGiST research group.
|
2024-12-11 |
|
rmblast
|
public |
RMBlast is a RepeatMasker compatible version of the standard NCBI BLAST+ suite.
|
2024-12-05 |
|
busco
|
public |
Assessment of assembly completeness using Universal Single Copy Orthologs.
|
2024-12-05 |
|
hicexplorer
|
public |
Set of programs to process, analyze and visualize Hi-C and capture Hi-C data
|
2024-11-28 |
|
svtopovz
|
public |
Complex structural variant visualization for HiFi sequencing data: plotting tool.
|
2024-11-19 |
|
gtotree
|
public |
GToTree is a user-friendly workflow for phylogenomics.
|
2024-11-13 |
