| Package Name | Access | Summary | Updated |
|---|---|---|---|
| bioconductor-hicrep | public | Measuring the reproducibility of Hi-C data | 2025-04-22 |
| takeabreak | public | tool that can detect inversion breakpoints directly from raw NGS reads, without the need of any reference genome and without de novo assembling the genomes | 2025-04-22 |
| nanolyse | public | Removing lambda DNA control reads from fastq dataset | 2025-04-22 |
| tantan | public | tantan masks simple regions (low complexity & short-period tandem repeats) in biological sequences. | 2025-04-22 |
| graphprot | public | GraphProt is a tool for modelling binding preferences of RNA-binding proteins from high-throughput experiments such as CLIP-seq and RNAcompete. | 2025-04-22 |
| bioconductor-copynumber | public | Segmentation of single- and multi-track copy number data by penalized least squares regression. | 2025-04-22 |
| perl-io-gzip | public | Perl extension to provide a PerlIO layer to gzip/gunzip | 2025-04-22 |
| kissplice | public | A local transcriptome assembler for SNPs, indels and AS events | 2025-04-22 |
| mapsembler2 | public | Targeted assembly software | 2025-04-22 |
| mentalist | public | The MLST pipeline developed by the PathOGiST research group. | 2025-04-22 |
| sis | public | A tool that uses mummer to scaffold small genomes. | 2025-04-22 |
| bio_hansel | public | Subtype Salmonella enterica genomes using 33bp k-mer typing schemes. | 2025-04-22 |
| bioconductor-scran | public | Methods for Single-Cell RNA-Seq Data Analysis | 2025-04-22 |
| bioconductor-biseq | public | Processing and analyzing bisulfite sequencing data | 2025-04-22 |
| bioconductor-globaltest | public | Testing Groups of Covariates/Features for Association with a Response Variable, with Applications to Gene Set Testing | 2025-04-22 |
| bioconductor-simpleaffy | public | Very simple high level analysis of Affymetrix data | 2025-04-22 |
| bioconductor-jaspar2014 | public | Data package for JASPAR | 2025-04-22 |
| perl-bio-cigar | public | Parse CIGAR strings and translate coordinates to/from reference/query | 2025-04-22 |
| perl-types-standard | public | bundled set of built-in types for Type::Tiny | 2025-04-22 |
| perl-pod-usage | public | Print a usage message from embedded pod documentation. | 2025-04-22 |
| xyalign | public | Command line tools and python library to infer ploidy, correct for sex chromosome complement, and work with NGS data | 2025-04-22 |
| perl-class-methodmaker | public | Create generic methods for OO Perl | 2025-04-22 |
| virema | public | ViReMa (Viral Recombination Mapper) detects and reports recombination or fusion events in virus genomes using deep sequencing datasets. | 2025-04-22 |
| r-george | public | geoRge, a computational tool for stable isotope labelling detection in LC/MS-based untargeted metabolomics | 2025-04-22 |
| ascat | public | ASCAT is a method to derive copy number profiles of tumour cells, accounting for normal cell admixture and tumour aneuploidy (Figure 1). ASCAT infers tumour purity (the fraction of tumour cells) and ploidy (the amount of DNA per tumour cell, expressed as multiples of haploid genomes) from SNP array or massively parallel sequencing data, and calculates whole-genome allele-specific copy number profiles (the number of copies of both parental alleles for all SNP loci across the genome). | 2025-04-22 |
