Frontend & Design · Bioinformatics

The Bandle package enables the analysis and visualisation of differential localisation experiments using mass-spectrometry data.

bioMate-AI/biomate-bioconductor-kb

Detect allele-specific chromatin accessibility from ATAC-seq using WASP, GATK ASEReadCounter, or RASQUAL.

GPTomics/bioSkills

Stage 5 of the spatial transcriptomics workflow — neighborhood enrichment and cell-cell communication analysis.

QING1105/ezST

Infer cis-regulatory connections (peak-to-peak co-accessibility) from scATAC-seq using Cicero, ArchR getCoAccessibility, or SCENIC+.

GPTomics/bioSkills

Predict enhancer-gene regulatory connections from ATAC-seq using ABC, ENCODE-rE2G, HiChIP, or Cicero.

GPTomics/bioSkills

Resolve the architecture of focal oncogene amplifications — extrachromosomal DNA (ecDNA), breakage-fusion-bridge (BFB) cycles, homogeneously staining regions (HSR), and linear amplification — from…

GPTomics/bioSkills

Post-translational modification analysis including phosphorylation, acetylation, and ubiquitination.

FreedomIntelligence/OpenClaw-Medical-Skills

Identify differentially accessible chromatin regions across conditions using DiffBind, csaw, DESeq2, or edgeR.

GPTomics/bioSkills

Analyze TF motif accessibility variability across samples or single cells using chromVAR.

GPTomics/bioSkills

Extracts cfDNA fragmentomics features (DELFI genome-wide short/long ratios, WPS nucleosome positioning, Griffin GC-corrected accessibility profiles, end-motifs/MDS, OCF) for cancer detection and…

GPTomics/bioSkills

Orchestrates the end-to-end bulk ATAC-seq pipeline from FASTQ to differential accessibility and TF footprints, chaining Nextera-aware fastp QC, Bowtie2 alignment, chrM removal, dedup, a single Tn5…

GPTomics/bioSkills

Auto-annotate plasmids with features (promoters, terminators, resistance, origins, tags, fluorescent proteins) via BLAST against curated DBs (Addgene, fpbase, SnapGene).

jaechang-hits/SciAgent-Skills

Frames PTM/phosphoproteomics analysis as three stacked inference layers on a biased enrichment - chemistry selection, site localization (FLR), and protein-level-adjusted quantification with…

GPTomics/bioSkills

Find differentially accessible chromatin regions between conditions using DiffBind or DESeq2.

FreedomIntelligence/OpenClaw-Medical-Skills

Analyze transcription factor motif accessibility variability using chromVAR.

FreedomIntelligence/OpenClaw-Medical-Skills

Predict RNA secondary structure, MFE folding, base-pair probabilities, RNA-RNA interactions via ViennaRNA Python bindings.

jaechang-hits/SciAgent-Skills

omicsViewer visualizes ExpressionSet (or SummarizedExperiment) in an interactive way.

bioMate-AI/biomate-bioconductor-kb

Statial is a suite of functions for identifying changes in cell state.

bioMate-AI/biomate-bioconductor-kb