| Package Name | Access | Summary | Updated |
|---|---|---|---|
| imods | public | toolkit to perform Normal Mode Analysis (NMA) in internal coordinates (IC) on both protein and nucleic acid atomic structures. | 2025-04-22 |
| hmftools-sigs | public | Fits sample SNV counts to trinucleotide signature definitions. | 2025-04-22 |
| hmftools-rose | public | ROSE makes an actionability summary of the clinical relevant (for the Netherlands) genomic events and signatures as determined by the Hartwig pipeline. | 2025-04-22 |
| graphmb | public | GraphMB is a Metagenomic Binner developed for long-read assemblies, that takes advantage of graph machine learning algorithms and the assembly graph generated during assembly. | 2025-04-22 |
| obonet | public | Parse OBO formatted ontologies into networkx | 2025-04-22 |
| hmftools-protect | public | PROTECT determines the clinical evidence applicable for a particular tumor sample based on all genomic events and signatures that are determined by the Hartwig pipeline. | 2025-04-22 |
| phaser | public | phASEr performs haplotype phasing and provides measures of haplotypic expression for RNA based assays. | 2025-04-22 |
| metagem | public | Generate context specific genome-scale metabolic models and predict metabolic interactions directly from metagenomic data | 2025-04-22 |
| hmftools-sv-prep | public | SV Prep generates a maximally filtered SV BAM file by identifying candidate SV junctions and extracting all reads that may provide support to that junction. | 2025-04-22 |
| authentict | public | Estimates present-day DNA contamination in ancient DNA single-stranded libraries. | 2025-04-22 |
| r-chromium | public | Toolkit for 10X Genomics Chromium single cell data. | 2025-04-22 |
| bactopia-teton | public | Methods used by Bactopia for taxonomic classification | 2025-04-22 |
| bactopia-variants | public | Methods used by Bactopia for SNP and InDel analysis | 2025-04-22 |
| insurveyor | public | An insertion caller for Illumina paired-end WGS data. | 2025-04-22 |
| shapeit5 | public | Fast and accurate method for estimation of haplotypes (phasing) | 2025-04-22 |
| drtransformer | public | Heuristic cotranscriptional folding using the nearest neighbor energy model. | 2025-04-22 |
| hmnqc | public | Compute differents metrics about quality, check identity and coverage from high-throughput sequencing provided by targeted NGS | 2025-04-22 |
| bactopia-assembler | public | The assembly process used by Bactopia. | 2025-04-22 |
| bactopia-gather | public | The methods used in Bactopia to gather all samples into one place | 2025-04-22 |
| bactopia-qc | public | The methods used in Bactopia for read QC | 2025-04-22 |
| bactopia-sketcher | public | Methods used by Bactopia for minmer sketching | 2025-04-22 |
| barseqcount | public | Analysis of DNA barcode sequencing experiments | 2025-04-22 |
| sem | public | A nucleosome calling package for nucleosome subtype detection | 2025-04-22 |
| dmbiolib | public | Library of Python functions for bioinformatics | 2025-04-22 |
| salty | public | SaLTy assigns a lineage to Staphylococcus aureus WGS data and is suitable for describing large-scale S. aureus genomic epidemiology. | 2025-04-22 |
