This page outlines the repositories under the NICHD-BSPC GitHub organization as well as other open-source repositories we maintain and/or contribute to. For other information about BSPC, please see the official NIH page for BSPC.
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Lee 2026: Code to reproduce the results Genome-wide crossover analysis in the holocentric pantry moth reveals strong crossover assurance and interference during spermatogenesis https://doi.org/10.1101/gr.281913.126
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Aksenova 2025: Code to reproduce the results from TREX2 component PCID2 scaffolds alternative SAC3-based subcomplexes with distinct RNA processing and export function, https://doi.org/10.64898/2026.04.13.716336
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Thongdee 2025: Code to reproduce the results from Modulation of protein activity by small RNA base pairing internal to coding sequences, https://doi.org/10.1016/j.molcel.2025.03.014
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lcdb-wf: our set of Snakemake workflows and downstream analysis code for RNA-seq-like, ChIP-seq-like, and variant calling.
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pybedtools: wraps and extends BEDTools for use in Python.
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gffutils: GTF and GFF gene annotation file manipulation and interconversion.
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trackhub: Build UCSC Genome Browser track hubs with Python.
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termseq-peaks: peak-calling for Term-seq data in bacterial genomes.
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carnation: R Shiny web app for exploring RNA-seq data
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cascade: R Shiny web app for exploring scRNA-seq and spatial transcriptomics data
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AnalyzeOlink: R package and more for analyzing Olink proximal extension assay data
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llm: containerized LLM agents on local and remote systems
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bacteria-dash: a generalization of the DASH rRNA depletion method (see original) to allow any species and any target locations.
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multiome-wf: a Snakemake workflow for combined scRNA-seq and scATAC-seq analysis; see documentation.
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Intro to RNA-seq: An adaptation of the Harvard Bioinformatics Core RNA-seq training materials to the NIH Biowulf high-performance compute cluster.
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BSPC training pages: curated links to bioinformatics training resources.
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daler/dotfiles: Batteries-included set of dotfiles used by BSPC and alumni
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bioconda-recipes: contributions to the Bioconda channel
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bioconda-utils: development and maintenance of the underlying infrastructure for the Bioconda channel
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bioconda-docs: documentation for the Bioconda channel