| Package Name | Access | Summary | Updated |
|---|---|---|---|
| clickclick | public | No Summary | 2025-03-25 |
| blossomv | public | Python wrapper for the Blossom V algorithm | 2025-03-25 |
| theta | public | Tumor Heterogeneity Analysis (THetA) is an algorithm that estimates the tumor purity and clonal/subclonal copy number aberrations directly from high-throughput DNA sequencing data. | 2025-03-25 |
| bnpy | public | Bayesian nonparametric machine learning for python. | 2025-03-25 |
| bicseq2-seg | public | No Summary | 2025-03-25 |
| bicseq2-norm | public | No Summary | 2025-03-25 |
| r-ada | public | Performs discrete, real, and gentle boost under both exponential and logistic loss on a given data set. The package ada provides a straightforward, well-documented, and broad boosting routine for classification, ideally suited for small to moderate-sized data sets. | 2025-03-25 |
| samblaster | public | A tool to mark duplicates and extract discordant and split reads from sam files. | 2025-03-25 |
| delly_utils | public | Structural variant discovery by integrated paired-end and split-read analysis | 2025-03-25 |
| remixt | public | ReMixT is a tool for joint inference of clone specific segment and breakpoint copy number in whole genome sequencing data | 2025-03-25 |
| biobambam2 | public | Tools for early stage alignment file processing | 2025-03-25 |
| libmaus2 | public | collection of data structures and algorithms | 2025-03-25 |
| libmaus | public | libmaus is a collection of data structures and algorithms | 2025-03-25 |
| boost_lib | public | Library for boost c++ | 2025-03-25 |
| citup | public | Clonality inference in multiple tumor samples using phylogeny | 2025-03-25 |
| shapeit | public | SHAPEIT is a fast and accurate method for estimation of haplotypes (aka phasing) from genotype or sequencing data. | 2025-03-25 |
| hmmcopy_utils | public | Utilities for HMMCopy | 2025-03-25 |
| gsl | public | No Summary | 2025-03-25 |
| clonehd | public | High-definition reconstruction of clonal composition from next-generation sequencing data | 2025-03-25 |
| bioconductor-titan | public | 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. | 2025-03-25 |
| r-argparse | public | A command line parser to be used with Rscript to write "#!" shebang scripts that gracefully accept positional and optional arguments and automatically generate usage. | 2025-03-25 |
| r-findpython | public | Package designed to find an acceptable python binary. | 2025-03-25 |
| bioconductor-hmmcopy | public | 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. | 2025-03-25 |
| defuse | public | Bioinformatics tool for gene fusion discovery using RNA-Seq data | 2025-03-25 |
| biowrappers | public | No Summary | 2025-03-25 |
