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Frontend & Design · GPTomics/bioSkills
Skills
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| # | Skill | Repository | Stars | Used in | Tokens | Auto-check | Licence | Updated |
|---|---|---|---|---|---|---|---|---|
| 1 | Detect allele-specific chromatin accessibility from ATAC-seq using WASP, GATK ASEReadCounter, or RASQUAL. | GPTomics/ | 1.2k | 2 repos | ~4.3k | Automated safety check: Pass | MIT | 1 mo ago |
| 2 | Infer cis-regulatory connections (peak-to-peak co-accessibility) from scATAC-seq using Cicero, ArchR getCoAccessibility, or SCENIC+. | GPTomics/ | 1.2k | 2 repos | ~4.6k | Automated safety check: Pass | MIT | 1 mo ago |
| 3 | Predict enhancer-gene regulatory connections from ATAC-seq using ABC, ENCODE-rE2G, HiChIP, or Cicero. | GPTomics/ | 1.2k | 2 repos | ~4.6k | Automated safety check: Pass | MIT | 1 mo ago |
| 4 | Resolve the architecture of focal oncogene amplifications — extrachromosomal DNA (ecDNA), breakage-fusion-bridge (BFB) cycles, homogeneously staining regions (HSR), and linear amplification — from… | GPTomics/ | 1.2k | 2 repos | ~2.8k | Automated safety check: Pass | MIT | 1 mo ago |
| 5 | Identify recurrent and driver copy number alterations across a tumor cohort with GISTIC2 (G-score, Ziggurat deconstruction, focal vs broad/arm-level analysis, q-values from permutation) and quantify… | GPTomics/ | 1.2k | 2 repos | ~3.2k | Automated safety check: Pass | MIT | 1 mo ago |
| 6 | Select colormaps and qualitative palettes for scientific figures using perceptual-uniformity, color-vision-deficiency safety, and luminance-monotonicity criteria. | GPTomics/ | 1.2k | 2 repos | ~3.6k | Automated safety check: Pass | MIT | 1 mo ago |
| 7 | Identify differentially accessible chromatin regions across conditions using DiffBind, csaw, DESeq2, or edgeR. | GPTomics/ | 1.2k | 2 repos | ~6k | Automated safety check: Pass | MIT | 1 mo ago |
| 8 | Analyze TF motif accessibility variability across samples or single cells using chromVAR. | GPTomics/ | 1.2k | 2 repos | ~5.2k | Automated safety check: Pass | MIT | 1 mo ago |
| 9 | 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/ | 1.2k | 1 repo | ~4.3k | Automated safety check: Pass | MIT | 1 mo ago |
| 10 | Detects cancer and infers tissue-of-origin from cfDNA methylation by choosing conversion chemistry (bisulfite vs EM-seq vs TAPS vs cfMeDIP), calling read-level methylation haplotypes rather than… | GPTomics/ | 1.2k | 1 repo | ~4.1k | Automated safety check: Pass | MIT | 1 mo ago |
| 11 | 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/ | 1.2k | 1 repo | ~4.1k | Automated safety check: Pass | MIT | 1 mo ago |
| 12 | 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/ | 1.2k | 1 repo | ~6.9k | Automated safety check: Pass | MIT | 1 mo ago |
