| Package Name | Access | Summary | Updated |
|---|---|---|---|
| r-biomark | public | Variable selection methods are provided for several classification methods: the lasso/elastic net, PCLDA, PLSDA, and several t-tests. Two approaches for selecting cutoffs can be used, one based on the stability of model coefficients under perturbation, and the other on higher criticism. | 2025-04-22 |
| bioconductor-rtcga.mrna | public | mRNA datasets from The Cancer Genome Atlas Project | 2025-04-22 |
| bioconductor-rtcga | public | The Cancer Genome Atlas Data Integration | 2025-04-22 |
| perl-http-server-simple | public | Lightweight HTTP server | 2025-04-22 |
| a5-miseq | public | A5-miseq is a pipeline for assembling DNA sequence data generated on the Illumina sequencing platform. This README will take you through the steps necessary for running _A5-miseq_ | 2025-04-22 |
| novobreak | public | local assembly for breakpoint detection in cancer genomes | 2025-04-22 |
| bioconductor-genefu | public | Computation of Gene Expression-Based Signatures in Breast Cancer | 2025-04-22 |
| bioconductor-cancersubtypes | public | Cancer subtypes identification, validation and visualization based on multiple genomic data sets | 2025-04-22 |
| bioconductor-srap | public | Simplified RNA-Seq Analysis Pipeline | 2025-04-22 |
| bioconductor-baalchip | public | BaalChIP: Bayesian analysis of allele-specific transcription factor binding in cancer genomes | 2025-04-22 |
| bioconductor-mirnatap.db | public | This package holds the database for miRNAtap. | 2025-04-22 |
| break-point-inspector | public | BPI uses Manta’s variant calls to re-analyse BAM files and precisely determine the location of the breaks, and applies a set of filters to remove false positives, thereby increasing the accuracy of Manta’s calls. | 2025-04-22 |
| bioconductor-gtrellis | public | Genome Level Trellis Layout | 2025-04-22 |
| bioconductor-mutationalpatterns | public | Comprehensive genome-wide analysis of mutational processes | 2025-04-22 |
| seq-seq-pan | public | seq-seq-pan | 2025-04-22 |
| sicer | public | A clustering approach for identification of enriched domains from histone modification ChIP-Seq data | 2025-04-22 |
| repenrich | public | RepEnrich is a method to estimate repetitive element enrichment using high-throughput sequencing data. | 2025-04-22 |
| r-maldirppa | public | Provides methods for quality control and robust pre-processing and analysis of MALDI mass spectrometry data. | 2025-04-22 |
| r-purbayes | public | PurBayes is an MCMC-based algorithm that uses next-generation sequencing data to estimate tumor purity and clonality for paired tumor-normal data. | 2025-04-22 |
| r-icluster | public | Integrative clustering of multiple genomic data types using a joint latent variable model. | 2025-04-22 |
| panx | public | Microbial pan-genome analysis and exploration tool | 2025-04-22 |
| r-metama | public | Combines either p-values or modified effect sizes from different studies to find differentially expressed genes | 2025-04-22 |
| bioconductor-flowbeads | public | flowBeads: Analysis of flow bead data | 2025-04-22 |
| perl-go-perl | public | perl modules for GO and other OBO ontologies | 2025-04-22 |
| pneumocat | public | PneumoCaT (Pneumococcal Capsular Typing) uses a two-step step approach to assign capsular type to S.pneumoniae genomic data (Illumina) | 2025-04-22 |
