Databases · GPTomics/bioSkills

Analyzes CUT&RUN (Skene Henikoff 2017) and CUT&Tag (Kaya-Okur 2019) chromatin profiling data.

GPTomics/bioSkills

Identifies differentially bound ChIP-seq regions between conditions using DiffBind, csaw (sliding windows), DESeq2/edgeR/PyDESeq2 on count matrices, NormR (control-aware), or MAnorm2.

GPTomics/bioSkills

Normalizes ChIP-seq data using exogenous spike-in (ChIP-Rx with Drosophila chromatin per Orlando 2014 / Egan 2016; E.

GPTomics/bioSkills

Normalize read-depth copy-ratio profiles and segment them into copy-number regions using circular binary segmentation (CBS, DNAcopy), hidden Markov models, HaarSeg, and fused-lasso methods.

GPTomics/bioSkills

Call copy number variants with the GATK best-practices workflows — the somatic CNV pipeline (CollectReadCounts, DenoiseReadCounts with tangent normalization, ModelSegments, CallCopyRatioSegments)…

GPTomics/bioSkills

Query and download from NCBI Gene Expression Omnibus (GEO) and EMBL-EBI's BioStudies/ArrayExpress mirror.

GPTomics/bioSkills

Bead-based signal normalization and cross-batch harmonization for CyTOF and high-parameter cytometry - EQ four-element bead normalization of instrument sensitivity drift (CATALYST normCytof…

GPTomics/bioSkills

Assigns honest lipid annotation levels, designs class-based internal-standard quantification, and runs lipid-aware differential and enrichment analysis with lipidr, guarding against…

GPTomics/bioSkills

Runs the MS-DIAL preprocessing workflow (peak picking, MS2Dec spectral deconvolution, alignment, gap-filling) and imports the alignment-result table into R or Python with honest filtering.

GPTomics/bioSkills

Designs QC, corrects signal drift, removes batch effects, filters features, normalizes samples, and imputes missing values for untargeted LC-MS/GC-MS metabolomics, framing each step as a measurement…

GPTomics/bioSkills

Turns raw Illumina Infinium methylation BeadChip IDATs (450K, EPIC, EPICv2) into a defensible beta/M matrix with sesame (openSesame/SigDF) or minfi (RGChannelSet - MethylSet - GenomicRatioSet).

GPTomics/bioSkills

Performs probe filtering and sample-level QC on Illumina Infinium methylation arrays (450K / EPIC / EPICv2) to decide which probes and samples to trust.

GPTomics/bioSkills

Imports Bismark coverage or cytosine-report files into the methylKit object model, then runs the import-to-results spine - filterByCoverage, normalizeCoverage, unite/destrand, calculateDiffMeth…

GPTomics/bioSkills

Stratifies patients into multi-omics subtypes by building one patient-by-patient similarity network per omic, fusing them with SNF's cross-network diffusion, and spectral-clustering the fused graph…

GPTomics/bioSkills

Processes experimental RNA structure probing data (SHAPE-MaP, DMS-MaPseq) into per-nucleotide reactivity profiles with ShapeMapper2, then uses them as soft restraints on thermodynamic folding.

GPTomics/bioSkills

Orchestrates the untargeted LC-MS metabolomics pipeline end-to-end (xcms 4.x feature extraction, QC/drift/normalization, confidence-stratified annotation, permutation-validated statistics…

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

Extracts, filters, annotates, and exports differential expression results from DESeq2 or edgeR with proper handling of padj=NA (independent filtering, Cook's outliers, all-zero), multiple-testing…

GPTomics/bioSkills

Normalizes and transforms RNA-seq count matrices for DE, visualization, clustering, and ML.

GPTomics/bioSkills

Compares Hi-C contact maps between conditions across the right scale -- differential bin-pair contacts (multiHiCcompare, diffHic), differential A/B compartments (dcHiC), differential TAD boundaries…

GPTomics/bioSkills

Harmonizes already-normalized per-omic matrices onto a common footing before joint integration - assembling a MultiAssayExperiment, choosing the per-omic variance-stabilizing transform, deciding…

GPTomics/bioSkills

Joint genotype a cohort of per-sample gVCFs with GATK (HaplotypeCaller -ERC GVCF - GenomicsDBImport or CombineGVCFs - GenotypeGVCFs) or GLnexus for DeepVariant gVCFs, producing a squared-off…

GPTomics/bioSkills

Left-align and trim indels to parsimonious canonical form, decompose MNPs (atomize), and split multiallelic variants with bcftools norm.

GPTomics/bioSkills