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Packages
| Name | Latest Version | Summary | Updated | License |
|---|
| bcftools | 1.6 | 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. | Mar 25, 2025 | MIT |
| bioconductor-hmmcopy | 1.20.0 | Corrects GC and mappability biases for readcounts (i.e. coverage) in non-overlapping windows of fixed length for single whole genome samples, yielding a rough estimate of copy number for furthur analysis. Designed for rapid correction of high coverage whole genome tumour and normal samples. | Mar 25, 2025 | GPL-3 |
| bioconductor-titancna | 1.16.0 | Hidden Markov model to segment and predict regions of subclonal copy number alterations (CNA) and loss of heterozygosity (LOH), and estimate cellular prevalenece of clonal clusters in tumour whole genome sequencing data. | Mar 25, 2025 | GPL-3 |
| bwa | 0.7.16 | The BWA read mapper. | Mar 25, 2025 | GPL3 |
| eagle-phase | 2.3.5 | The Eagle software estimates haplotype phase either within a genotyped cohort or using a phased reference panel | Mar 25, 2025 | GPLv3 |
| hmmcopy | 0.1.1 | C++ based programs for analyzing BAM files and preparing read counts -- used with bioconductor-hmmcopy | Mar 25, 2025 | GPL-3 |
| kallisto | 0.43.1 | Quantifying abundances of transcripts from RNA-Seq data, or more generally of target sequences using high-throughput sequencing reads. | Mar 25, 2025 | BSD_2_Clause |
| mixcr | 2.1.3 | MiXCR is a universal software for fast and accurate analysis of raw T- or B- cell receptor repertoire sequencing data. | Mar 25, 2025 | https://github.com/milaboratory/mixcr/blob/develop/LICENSE |
| msgf_plus | 2017.07.21 | MS-GF+ is a new MS/MS database search tool that is sensitive (it identifies more peptides than other database search tools and as many peptides as spectral library search tools) and universal (works well for diverse types of spectra, different configurations of MS instruments and different experimental protocols). | Mar 25, 2025 | https://github.com/sangtaekim/msgfplus/blob/master/LICENSE.txt |
| opossum | 0.2.0de259b45a35cd7d4c01dbb40d48d16c9118d76c4 | — | Mar 25, 2025 | GPLv3 |
| optitype | 1.2.1 | Precision HLA typing from next-generation sequencing data | Mar 25, 2025 | BSD |
| percolator | 3.1 | — | Mar 25, 2025 | — |
| platypus-variant | 0.8.1.1 | A Haplotype-Based Variant Caller For Next Generation Sequence Data | Mar 25, 2025 | GPLv3 |
| proteowizard | 3_0_9992 | — | Mar 25, 2025 | — |
| sambamba | 0.6.6 | Tools for working with SAM/BAM data | Mar 25, 2025 | GPLv2 |
| samtools | 1.6 | Tools for dealing with SAM, BAM and CRAM files | Mar 25, 2025 | MIT |
| snpeff | 4.3.1r | Genetic variant annotation and effect prediction toolbox | Mar 25, 2025 | LGPLv3 |
| snpsift | 4.3.1r | Toolbox that allows you to filter and manipulate annotated files | Mar 25, 2025 | LGPLv3 |
| star | 2.5.3a | An RNA-seq read aligner. | Mar 25, 2025 | GPLv3 |
| strelka | 2.8.4 | Strelka calls somatic and germline small variants from mapped sequencing reads | Mar 25, 2025 | GPLv3 |
| stringtie | 1.3.3 | Transcriptome assembly and quantification for RNA-seq | Mar 25, 2025 | Artistic License 2.0 |
| subread | 1.6.0 | High-performance read alignment, quantification, and mutation discovery | Mar 25, 2025 | GPLv3 |
| transdecoder | 3.0.1 | TransDecoder identifies candidate coding regions within transcript sequences, such as those generated by de novo RNA-Seq transcript assembly using Trinity, or constructed based on RNA-Seq alignments to the genome using Tophat and Cufflinks. | Mar 25, 2025 | Broad Institute |
| ucsc-bedgraphtobigwig | 357 | Convert a bedGraph file to bigWig format. | Mar 25, 2025 | varies; see http://genome.ucsc.edu/license |
| varscan | 2.4.3 | variant detection in massively parallel sequencing data | Mar 25, 2025 | The Non-Profit Open Software License version 3.0 (NPOSL-3.0) |