| Package Name | Access | Summary | Updated |
|---|---|---|---|
| r-connectpdb | public | Database connector functions for PathogenDB and PSP | 2026-03-19 |
| scrnaseq-anndata-utils | public | Utilities for handling scRNAseq AnnData objects. | 2026-03-18 |
| scrinvex | public | SCRINVEX - A Single Cell RNA-Seq QC tool | 2025-12-30 |
| amplicon_sorter | public | Conda package for amplicon_sorter, https://github.com/avierstr/amplicon_sorter. | 2025-12-22 |
| cirrocumulus | public | No Summary | 2025-12-22 |
| symphonypy | public | No Summary | 2025-12-21 |
| azimuth-transfer-tool | public | Azimuth dual-reference transfer with Bioconductor dependency resolution. | 2025-12-21 |
| isopropeller | public | Code for isoPropeller isoform analysis. | 2025-11-30 |
| omics-pipelines | public | Pipelines to analyze different types of genomics data. | 2025-08-17 |
| omics-toolkit | public | Collection of scripts and utilities to analyze various types of 'omics data. | 2025-08-17 |
| omics-bintools | public | Static builds of various bioinformatics utilities. | 2025-08-03 |
| omics-ucsc-utils | public | Static build of kent ucsc-utils. | 2025-03-25 |
| omics-splicing | public | Wrapper scripts for differential splicing analyses. | 2025-03-25 |
| omics-megena | public | Wrapper scripts for megena co-expression network analyses. | 2025-03-25 |
| minerva-queue-lsf | public | Collection of scripts to make it easier to interact with the queueing system on the Icahn School of Medicine 'Minerva' cluster. | 2025-03-25 |
| r-dropletqc | public | This simple R package can be used to calculate a useful QC metric for single cell RNA-seq datasets generated with the 10x Genomics Chromium Single Cell Gene Expression platform: the nuclear fraction score. This score captures, for each input cell barcode, the fraction of RNA that likely originated from unspliced (nuclear) pre-mRNA. Sheared cell membranes from damaged cells in the input cell suspension primarily release cytoplasmic RNA into solution, while the nuclear envelope remains intact. As a result, RNA released from stressed or damaged cells consists mostly of mature cytoplasmic mRNA and is relatively depleted of unspliced nuclear precursor mRNA. This fact can be useful in identifying both; droplets containing only ambient RNA, characterised by a low nuclear fraction score, and damaged cells, which can be identified by a high score. The QC metric is calculated by parsing the input barcoded BAM file for CB and RE flags added by 10x Genomics' Cell Ranger software. | 2025-03-25 |
