gptomics/bioskills

1

bio-single-cell-metabolite-communication Infers metabolite-mediated cell-cell communication from scRNA-seq by scoring enzyme-to-sensor pairs (MEBOCOST), with …

gptomics/bioskills

2

2

bio-spatial-transcriptomics-spatial-proteomics Analyzes multiplexed antibody-imaging data (CODEX/PhenoCycler, MIBI-TOF, IMC, CyCIF, Opal/Vectra mIF) as continuous p…

gptomics/bioskills

2

3

bio-causal-genomics-mendelian-randomization Estimate causal effects of an exposure on an outcome from GWAS summary statistics using genetic instruments. Implemen…

gptomics/bioskills

1

4

bio-clinical-biostatistics-logistic-regression Performs logistic regression for clinical trial outcomes (binary, ordinal, multinomial) with marginal-vs-conditional …

gptomics/bioskills

1

5

bio-clinical-biostatistics-missing-data Implements missing-data sensitivity analyses for confirmatory clinical trials including MMRM under MAR (with Kenward-…

gptomics/bioskills

1

6

bio-clinical-biostatistics-survival-analysis Performs time-to-event analysis for clinical trials including Cox proportional hazards regression with PH diagnostics…

gptomics/bioskills

1

7

bio-data-visualization-genome-browser-tracks Generate genome browser visualizations using pyGenomeTracks or IGV batch scripting for publication figures. Use when …

gptomics/bioskills

1

8

bio-data-visualization-upset-plots Create UpSet plots to visualize set intersections as an alternative to Venn diagrams using UpSetR or upsetplot. Use w…

gptomics/bioskills

1

9

bio-data-visualization-volcano-customization Create publication-ready volcano plots with custom thresholds, gene labels, and highlighting using ggplot2, EnhancedV…

gptomics/bioskills

1

10

bio-differential-expression-de-results Extracts, filters, annotates, and exports differential expression results from DESeq2 or edgeR with proper handling o…

gptomics/bioskills

1

11

bio-differential-expression-de-visualization Creates DE-specific diagnostic and result visualizations using DESeq2/edgeR built-in functions and lightweight ggplot…

gptomics/bioskills

1

12

bio-differential-expression-deseq2-basics Performs differential expression on bulk RNA-seq count data with DESeq2's negative-binomial GLM, Wald and LRT testing…

gptomics/bioskills

1

13

bio-differential-expression-edger-basics Performs differential expression on bulk RNA-seq count data with edgeR's negative-binomial GLM and quasi-likelihood F…

gptomics/bioskills

1

14

bio-expression-matrix-normalization Normalizes and transforms RNA-seq count matrices for DE, visualization, clustering, and ML. Covers between-sample (TM…

gptomics/bioskills

1

15

bio-gene-regulatory-networks-coexpression-networks Build weighted gene co-expression networks to identify modules of co-regulated genes, relate them to phenotypes, and …

gptomics/bioskills

1

16

bio-gene-regulatory-networks-scenic-regulons Infer transcription factor regulons from single-cell RNA-seq with pySCENIC by combining GRNBoost2 co-expression, cisT…

gptomics/bioskills

1

17

bio-spatial-transcriptomics-high-resolution-binning Reconstructs single cells from sub-cellular spatial capture units (Visium HD 2um bins, Stereo-seq DNB spots, Slide-se…

gptomics/bioskills

1

18

bio-workflows-biomarker-pipeline End-to-end biomarker discovery workflow from expression data to validated biomarker panels. Covers feature selection …

gptomics/bioskills

1

19

bio-workflows-causal-genomics-pipeline End-to-end post-GWAS causal inference pipeline orchestrating heritability partitioning, genetic correlation, Mendelia…

gptomics/bioskills

1