Best bioinformatics skills, page 15

Authors bioinformatics pipelines in WDL (Workflow Description Language) run by Cromwell or miniwdl, targeting the GATK/Broad and Terra/AnVIL/BioData Catalyst cloud ecosystem, with tasks, workflows…

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

Orchestrates the end-to-end ChIP-seq pipeline from FASTQ to blacklist-filtered, annotated peaks, chaining fastp QC, Bowtie2 alignment, pre-dedup library-complexity QC (NRF/PBC), duplicate removal…

GPTomics/bioSkills

Orchestrates an end-to-end CRISPR editing experiment design from target gene to delivery-ready, validatable constructs.

GPTomics/bioSkills

Orchestrates an end-to-end de novo genome assembly project, routing each step to the right genome-assembly skill rather than restating it.

GPTomics/bioSkills

Orchestrates the GWAS pipeline from genotypes to association results, chaining PLINK2 QC (variant-then-sample missingness, controls-only HWE, KING relatedness), panel harmonization + joint…

GPTomics/bioSkills

Orchestrates imaging mass cytometry from raw MCD acquisitions to patient-level spatial analysis, chaining steinbock preprocessing, Mesmer/Cellpose segmentation, single-cell quantification…

GPTomics/bioSkills

Orchestrates the cell-free DNA / liquid-biopsy pipeline from plasma sequencing to tumor monitoring, forking tumor-naive (screening) vs tumor-informed (MRD), and chaining pre-analytic QC, UMI/duplex…

GPTomics/bioSkills

Orchestrates an end-to-end long-read structural-variant pipeline - basecalling to minimap2 alignment (platform-matched preset) to Sniffles2/cuteSV/pbsv calling to optional assembly-based calling…

GPTomics/bioSkills

Orchestrates genome-scale metabolic modeling from a protein FASTA to flux predictions, chaining CarveMe/gapseq reconstruction, memote QC, gap-filling, media-constrained FBA/FVA, gene essentiality…

GPTomics/bioSkills

End-to-end shotgun metagenomics workflow from FASTQ to taxonomic and functional profiles, orchestrating controls/host depletion, Kraken2+Bracken classification, MetaPhlAn marker profiling, and…

GPTomics/bioSkills

Orchestrates the end-to-end bisulfite/EM-seq methylation pipeline from FASTQ to differentially methylated regions, chaining Trim Galore/fastp QC, Bismark alignment + deduplication, methylation…

GPTomics/bioSkills

Orchestrates the end-to-end 10x Multiome (paired scRNA + scATAC) pipeline from Cell Ranger ARC output to a jointly-embedded, annotated object, chaining per-modality QC, AMULET fragment-based ATAC…

GPTomics/bioSkills

Orchestrates bottom-up proteomics from a search engine's output (MaxQuant/FragPipe/DIA-NN) to differential protein abundance with limma/DEqMS/MSstats.

GPTomics/bioSkills

Orchestrates the end-to-end bulk RNA-seq differential-expression pipeline from FASTQ to an annotated DE gene table, chaining fastp QC/trim, Salmon (decoy-aware) or STAR+featureCounts quantification…

GPTomics/bioSkills

Orchestrates the end-to-end single-cell RNA-seq pipeline from 10x Cell Ranger output to annotated cell types, chaining ambient-RNA removal, doublet detection, MAD-adaptive QC, normalization…

GPTomics/bioSkills

Orchestrates the end-to-end small RNA-seq pipeline from FASTQ to differential miRNAs and expression-filtered targets, chaining kit-aware cutadapt trimming (adapter on every read, UMI/4N handling)…

GPTomics/bioSkills

Orchestrates the end-to-end spatial transcriptomics pipeline from Space Ranger / vendor output to spatial domains and statistics, branching FIRST on platform class (imaging in-situ…

GPTomics/bioSkills

Orchestrates the end-to-end bulk short-read alternative-splicing pipeline from FASTQ to differential splicing, chaining fastp QC, cohort-consistent STAR 2-pass alignment (one shared junction DB)…

GPTomics/bioSkills

Orchestrates an end-to-end immune-repertoire pipeline from FASTQ to clonotypes, diversity, overlap, somatic hypermutation and lineages, routing on two forks.

GPTomics/bioSkills

Checklist-style reference for OmicVerse downstream tutorials covering AUCell scoring, metacell DEG, and related exports.

FreedomIntelligence/OpenClaw-Medical-Skills

Automated scRNA-seq cell type annotation via pre-trained logistic regression.

jaechang-hits/SciAgent-Skills

ENCODE Portal REST API for regulatory genomics: TF ChIP-seq, ATAC-seq/DNase-seq peaks, histone marks, and RNA-seq across 1000+ cell types.

jaechang-hits/SciAgent-Skills

Consensus cell type annotation: runs 10+ algorithms (KNN-Harmony/BBKNN/Scanorama/scVI, CellTypist, ONCLASS, Random Forest, SCANVI, SVM, XGBoost) on a labeled reference and transfers labels via…

jaechang-hits/SciAgent-Skills

Query ReMap 2022 TF ChIP-seq peak database via REST API and BED downloads.

jaechang-hits/SciAgent-Skills

# bioinformatics-init-analysis

LigphiDonk/Oh-my--paper

Use omicverse's pyComBat wrapper to remove batch effects from merged bulk RNA-seq or microarray cohorts, export corrected matrices, and benchmark pre/post correction visualisations.

FreedomIntelligence/OpenClaw-Medical-Skills

Turn bulk RNA-seq cohorts into synthetic single-cell datasets using omicverse's Bulk2Single workflow for cell fraction estimation, beta-VAE generation, and quality control comparisons against…

FreedomIntelligence/OpenClaw-Medical-Skills

Walk Claude through PyDESeq2-based differential expression, including ID mapping, DE testing, fold-change thresholding, and enrichment visualisation.

FreedomIntelligence/OpenClaw-Medical-Skills

Extend scRNA-seq developmental trajectories with BulkTrajBlend by generating intermediate cells from bulk RNA-seq, training beta-VAE and GNN models, and interpolating missing states.

FreedomIntelligence/OpenClaw-Medical-Skills

Guide Claude through SCSA, MetaTiME, CellVote, CellMatch, GPTAnno, and weighted KNN transfer workflows for annotating single-cell modalities.

FreedomIntelligence/OpenClaw-Medical-Skills

Run omicverse's CellPhoneDB v5 wrapper on annotated single-cell data to infer ligand-receptor networks and produce CellChat-style visualisations.

FreedomIntelligence/OpenClaw-Medical-Skills

Guide Claude through omicverse's single-cell clustering workflow, covering preprocessing, QC, multimethod clustering, topic modeling, cNMF, and cross-batch integration as demonstrated in…

FreedomIntelligence/OpenClaw-Medical-Skills

Walk through omicverse's single-cell preprocessing tutorials to QC PBMC3k data, normalise counts, detect HVGs, and run PCA/embedding pipelines on CPU, CPU–GPU mixed, or GPU stacks.

FreedomIntelligence/OpenClaw-Medical-Skills

Guide users through omicverse's spatial transcriptomics tutorials covering preprocessing, deconvolution, and downstream modelling workflows across Visium, Visium HD, Stereo-seq, and Slide-seq…

FreedomIntelligence/OpenClaw-Medical-Skills

Transcriptome-wide virtual spatial transcriptomics from H&E histology with DeepSpot-M.

ClawBio/ClawBio

ClawBio wrapper around nf-core/sarek 3.8.1 covering mapping through annotation for germline, tumor-only, and somatic paired analyses.

ClawBio/ClawBio

Wrapper skill for running nf-core/scrnaseq 4.1.0 upstream single-cell RNA-seq preprocessing from FASTQ with strict preflight, reproducibility outputs, and downstream handoff to ClawBio scRNA skills.

ClawBio/ClawBio

Query metadata and download data from ArrayExpress, EMBL-EBI's functional genomics collection, now hosted inside BioStudies.

ClawBio/ClawBio

RNA velocity analysis with scVelo. An agent skill from lamm-mit/scienceclaw.

lamm-mit/scienceclaw

Analyze single-cell RNA-seq at million-cell scale with Scarf: out-of-core Zarr stores on disk or object storage, provenance-tracked artifacts, audited QC, clustering, markers and donor comparisons.

sickn33/agentic-awesome-skills

NCBI GEO access via GEOparse and E-utilities. An agent skill from jaechang-hits/SciAgent-Skills.

jaechang-hits/SciAgent-Skills

Unified CLI/Python interface to 20+ genomic databases. An agent skill from jaechang-hits/SciAgent-Skills.

jaechang-hits/SciAgent-Skills

Open-source FAIR biology data framework. An agent skill from jaechang-hits/SciAgent-Skills.

jaechang-hits/SciAgent-Skills

Best practices for single-cell RNA-seq cell type annotation including marker-based, reference-based, and automated classification approaches.

jaechang-hits/SciAgent-Skills

The BloodGen3Module package provides functions for R user performing module repertoire analyses and generating fingerprint representations.

bioMate-AI/biomate-bioconductor-kb

Build, modify, and diagram SimBiology models — API reference, helper functions, and layout patterns.

matlab/matlab-agentic-toolkit

NCBI Gene via E-utilities: curated records across 1M+ taxa. An agent skill from jaechang-hits/SciAgent-Skills.

jaechang-hits/SciAgent-Skills