gptomics/bioskills

1

bio-population-genetics-selection-statistics Detect signatures of natural selection using Fst, Tajima's D, iHS, XP-EHH, and other selection statistics. Calculate …

gptomics/bioskills

3

2

bio-proteomics-dia-analysis Data-independent acquisition (DIA) proteomics analysis with DIA-NN and other tools. Use when analyzing DIA mass spect…

gptomics/bioskills

3

3

bio-proteomics-proteomics-qc Quality control and assessment for proteomics data. Use when evaluating proteomics data quality before downstream ana…

gptomics/bioskills

3

4

bio-proteomics-quantification Protein quantification from mass spectrometry data including label-free (LFQ, intensity-based), isobaric labeling (TM…

gptomics/bioskills

3

5

bio-proteomics-spectral-libraries Build, manage, and search spectral libraries for proteomics. Use when creating or working with spectral libraries for…

gptomics/bioskills

3

6

bio-read-alignment-bowtie2-alignment Align short reads using Bowtie2 with local or end-to-end modes. Supports gapped alignment. Use when aligning ChIP-seq…

gptomics/bioskills

3

7

bio-read-alignment-bwa-alignment Align DNA short reads to reference genomes using bwa-mem2, the faster successor to BWA-MEM. Use when aligning DNA sho…

gptomics/bioskills

3

8

bio-read-alignment-hisat2-alignment Align RNA-seq reads with HISAT2, a memory-efficient splice-aware aligner. Use when STAR's memory requirements are too…

gptomics/bioskills

3

9

bio-read-alignment-star-alignment Align RNA-seq reads with STAR (Spliced Transcripts Alignment to a Reference). Supports two-pass mode for novel splice…

gptomics/bioskills

3

10

bio-read-qc-adapter-trimming Remove sequencing adapters from FASTQ files using Cutadapt and Trimmomatic. Supports single-end and paired-end reads,…

gptomics/bioskills

3

11

bio-read-qc-contamination-screening Detect sample contamination and cross-species reads using FastQ Screen. Screen reads against multiple reference genom…

gptomics/bioskills

3

12

bio-read-qc-quality-filtering Filter reads by quality scores, length, and N content using Trimmomatic and fastp. Apply sliding window trimming, rem…

gptomics/bioskills

3

13

bio-read-qc-quality-reports Generate and interpret quality reports from FASTQ files using FastQC and MultiQC. Assess per-base quality, adapter co…

gptomics/bioskills

3

14

bio-read-qc-umi-processing Extract, process, and deduplicate reads using Unique Molecular Identifiers (UMIs) with umi_tools. Use when library pr…

gptomics/bioskills

3

15

bio-reporting-figure-export Exports publication-ready figures in various formats with proper resolution, sizing, and typography. Use when prepari…

gptomics/bioskills

3

16

bio-reporting-quarto-reports Build reproducible scientific documents, presentations, and websites with Quarto supporting R, Python, Julia, and Obs…

gptomics/bioskills

3

17

bio-restriction-enzyme-selection Select restriction enzymes by criteria using Biopython Bio.Restriction. Find enzymes that cut once, don't cut, produc…

gptomics/bioskills

3

18

bio-restriction-fragment-analysis Analyze restriction digest fragments using Biopython Bio.Restriction. Predict fragment sizes, get fragment sequences,…

gptomics/bioskills

3

19

bio-restriction-mapping Create restriction maps showing enzyme cut positions on DNA sequences using Biopython Bio.Restriction. Visualize cut …

gptomics/bioskills

3

20

bio-restriction-sites Find restriction enzyme cut sites in DNA sequences using Biopython Bio.Restriction. Search with single enzymes, batch…

gptomics/bioskills

3

21

bio-rna-quantification-tximport-workflow Import transcript-level quantifications from Salmon/kallisto/RSEM into R for gene-level analysis with DESeq2/edgeR us…

gptomics/bioskills

3

22

bio-spatial-transcriptomics-spatial-data-io Loads spatial transcriptomics data from Visium, Visium HD, Xenium, MERFISH/MERSCOPE, CosMx, Slide-seq/Curio, and Ster…

gptomics/bioskills

3

23

bio-spatial-transcriptomics-spatial-deconvolution Estimates per-spot cell type composition of spatial transcriptomics mixtures (Visium, Slide-seq, Stereo-seq) from an …

gptomics/bioskills

3

24

bio-spatial-transcriptomics-spatial-domains Identify spatially coherent tissue domains (regions like cortical layers, tumor vs stroma) in Visium, Visium HD, Xeni…

gptomics/bioskills

3

25

bio-spatial-transcriptomics-spatial-multiomics Integrates spatial RNA with a second modality (protein, ATAC, or histone marks) on spatial CITE-seq, DBiT-seq, spatia…

gptomics/bioskills

3

26

bio-spatial-transcriptomics-spatial-preprocessing Quality control, filtering, and normalization for spatial transcriptomics (Visium, Visium HD, Xenium, MERFISH/MERSCOP…

gptomics/bioskills

3

27

bio-spatial-transcriptomics-spatial-statistics Detects spatially variable genes, spatial autocorrelation, and cell-type colocalization for spatial transcriptomics u…

gptomics/bioskills

3

28

bio-spatial-transcriptomics-spatial-visualization Plots spatial transcriptomics expression, clusters, and annotations on tissue using Squidpy and Scanpy. Use when choo…

gptomics/bioskills

3

29

bio-structural-biology-alphafold-predictions Access and analyze AlphaFold protein structure predictions. Use when predicted structures are needed for proteins wit…

gptomics/bioskills

3

30

bio-structural-biology-modern-structure-prediction Predict protein structures using modern ML models including AlphaFold3, ESMFold, Chai-1, and Boltz-1. Use when predic…

gptomics/bioskills

3

31

bio-variant-calling-joint-calling Joint genotype calling across multiple samples using GATK CombineGVCFs and GenotypeGVCFs. Essential for cohort studie…

gptomics/bioskills

3

32

bio-vcf-statistics Generate variant statistics, sample concordance, and quality metrics using bcftools stats and gtcheck. Use when evalu…

gptomics/bioskills

3

33

bio-workflow-management-nextflow-pipelines Create scalable, containerized bioinformatics pipelines with Nextflow DSL2 supporting Docker, Singularity, and cloud …

gptomics/bioskills

3

34

bio-workflow-management-wdl-workflows Create portable bioinformatics pipelines with Workflow Description Language (WDL) using Cromwell or miniwdl execution…

gptomics/bioskills

3

35

bio-workflows-chipseq-pipeline End-to-end ChIP-seq workflow from FASTQ files to annotated peaks. Covers QC, alignment, peak calling with MACS3, and …

gptomics/bioskills

3

36

bio-workflows-clip-pipeline End-to-end CLIP-seq analysis from FASTQ to binding sites and motif enrichment. Use when analyzing protein-RNA interac…

gptomics/bioskills

3

37

bio-workflows-gwas-pipeline End-to-end GWAS workflow from VCF to association results. Covers PLINK QC, population structure correction, and assoc…

gptomics/bioskills

3

38

bio-workflows-imc-pipeline End-to-end imaging mass cytometry workflow from raw acquisitions to spatial cell analysis. Orchestrates image preproc…

gptomics/bioskills

3

39

bio-workflows-metabolomics-pipeline End-to-end metabolomics workflow from raw MS data to pathway analysis. Orchestrates XCMS preprocessing, annotation, n…

gptomics/bioskills

3

40

bio-workflows-methylation-pipeline End-to-end bisulfite sequencing workflow from FASTQ to differentially methylated regions. Covers Bismark alignment, m…

gptomics/bioskills

3

41

bio-workflows-multi-omics-pipeline End-to-end multi-omics integration workflow. Orchestrates data harmonization, MOFA/mixOmics integration, factor inter…

gptomics/bioskills

3

42

bio-workflows-multiome-pipeline End-to-end multiome workflow for joint scRNA-seq + scATAC-seq analysis. Covers data loading, separate modality proces…

gptomics/bioskills

3

43

bio-workflows-spatial-pipeline End-to-end spatial transcriptomics workflow for Visium/Xenium data. Covers data loading, preprocessing, spatial analy…

gptomics/bioskills

3

44

bio-workflows-tcr-pipeline End-to-end TCR/BCR repertoire analysis from FASTQ to clonotype diversity metrics. Use when analyzing immune repertoir…

gptomics/bioskills

3

45

bio-experimental-design-multiple-testing Applies multiple testing correction methods including FDR, Bonferroni, and q-value for genomics data. Use when filter…

gptomics/bioskills

2

46

bio-reporting-automated-qc-reports Generates standardized quality control reports by aggregating metrics from FastQC, alignment, and other tools using M…

gptomics/bioskills

2

47

bio-reporting-jupyter-reports Creates reproducible Jupyter notebooks for bioinformatics analysis with parameterization using papermill. Use when ge…

gptomics/bioskills

2

48

bio-single-cell-cnv-inference Infer large-scale copy-number alterations from tumor single-cell or single-nucleus RNA-seq to separate malignant from…

gptomics/bioskills

2

49

bio-single-cell-differential-abundance Test whether cell-type proportions or composition changed between conditions in single-cell data using Milo (miloR), …

gptomics/bioskills

2

50

bio-single-cell-hashing-demultiplexing Assign cells to their sample of origin from cell or nucleus hashing (CITE-seq HTOs, MULTI-seq lipid/cholesterol tags,…

gptomics/bioskills

2