| Package Name | Access | Summary | Updated |
|---|---|---|---|
| r-locuszoomr | public | Publication-ready regional gene locus plots similar to those produced by the web interface 'LocusZoom' <https://my.locuszoom.org>, but running locally in R. Genetic or genomic data with gene annotation tracks are plotted via R base graphics, 'ggplot2' or 'plotly', allowing flexibility and easy customisation including laying out multiple locus plots on the same page. It uses the 'LDlink' API <https://ldlink.nih.gov/?tab=apiaccess> to query linkage disequilibrium data from the 1000 Genomes Project and can overlay this on plots. | 2025-04-22 |
| kestrel | public | Mapping-free variant caller for short-read Illumina data | 2025-04-22 |
| tttrlib | public | A file format agnostic library for time-resolved imaging and spectroscopic data. | 2025-04-22 |
| gzrt | public | Unofficial build of the gzip Recovery Toolkit aka gzrecover. | 2025-04-22 |
| lamps | public | Liverpool Annotation of metabolites using Mass Spectrometry | 2025-04-22 |
| r-remapenrich | public | Bioinformatics tools to compute statistical enrichment of geonomic regions for ReMap peaks | 2025-04-22 |
| minimac4 | public | Computationally efficient genotype imputation | 2025-04-22 |
| bam2plot | public | Plot of coverage from bam file | 2025-04-22 |
| halfdeep | public | Automated detection of intervals covered at half depth by sequenced reads. | 2025-04-22 |
| orthodb | public | Interface to OrthoDB REST API. | 2025-04-22 |
| fc | public | Accurate Assembly of Full-length Consensus for Viral Quasispecies. | 2025-04-22 |
| rotate | public | Simple program to rotate a circular sequence to start at a given position or string. | 2025-04-22 |
| ntstat | public | a toolkit for statistical analysis of k-mer frequency and depth | 2025-04-22 |
| eagle2 | public | The Eagle software estimates haplotype phase either within a genotyped cohort or using a phased reference panel. | 2025-04-22 |
| meta-neuro | public | Medial Tractography Analysis (MeTA) | 2025-04-22 |
| msa4u | public | A simple visualisation tool for Multiple Sequence Alignment. | 2025-04-22 |
| amplici | public | AmpliCI: Cluster amplicon sequences in a fastq file with or without UMIs. | 2025-04-22 |
| ampd-up | public | De novo antimicrobial peptide sequence generation with recurrent neural networks | 2025-04-22 |
| doubletdetection | public | Method to detect and enable removal of doublets from single-cell RNA-sequencing. | 2025-04-22 |
| phenograph | public | Graph-based clustering for high-dimensional single-cell data. | 2025-04-22 |
| stxtyper | public | Accurately type both known and unknown Shiga toxin operons from assembled genomic sequence. | 2025-04-22 |
| jarvis3 | public | Improved encoder for genomic sequences. | 2025-04-22 |
| deepchopper-cli | public | A CLI for Genomic Language Model for Chimera Artifact Detection in Nanopore Direct RNA Sequencing. | 2025-04-22 |
| pyscenic | public | Python implementation of the SCENIC pipeline for transcription factor inference from single-cell transcriptomics experiments. | 2025-04-22 |
| coptr | public | Accurate and robust inference of microbial growth dynamics from metagenomic sequencing reads. | 2025-04-22 |
