Best bioinformatics skills, page 11

A skill your agent uses when analyzing bulk RNA-seq or microarray expression data to identify differentially expressed genes between two biological groups (case vs control), with volcano plots and…

aipoch/medical-research-skills

Access Ensembl REST API for vertebrate genomic data; use when you need gene/ID lookups, sequence retrieval, variant effect prediction (VEP), or homology/assembly coordinate mapping.

aipoch/medical-research-skills

A skill your agent uses to compute ESTIMATE immune-related microenvironment scores from a bulk expression matrix, generate an ESTIMATE score heatmap, and optionally generate group-wise ESTIMATE…

aipoch/medical-research-skills

ETE (Environment for Tree Exploration) toolkit for phylogenetic and hierarchical tree analysis; use it when you need to parse/manipulate Newick/NHX trees, detect duplication/speciation events…

aipoch/medical-research-skills

A skill your agent uses when validating an existing prognostic risk signature on an external bulk expression cohort with survival outcomes, producing risk scores, Kaplan-Meier curves, risk…

aipoch/medical-research-skills

A skill your agent uses when normalizing bulk gene or protein expression matrices with log2 transform, z-score standardization, or min-max scaling before downstream visualization or exploratory…

aipoch/medical-research-skills

Search for gene expression DataSets and Profiles in the NCBI GEO database.

aipoch/medical-research-skills

Unified CLI/Python interface for querying genomic, proteomic, structure, and expression data across 20+ bioinformatics databases; use when you need fast, scriptable retrieval by gene/protein IDs or…

aipoch/medical-research-skills

A skill your agent uses to run GSVA or ssGSEA pathway-level differential analysis from a bulk expression matrix and a sample group file, then generate a heatmap from the saved GSVA result object.

aipoch/medical-research-skills

A skill your agent uses when building a sample-level hierarchical clustering dendrogram from a bulk expression matrix and sample annotation table, especially for QC, batch inspection, or sample…

aipoch/medical-research-skills

A skill your agent uses when filtering genes with high missingness and then imputing missing values in a bulk expression matrix with group-aware KNN through DMwR2, where donor samples are restricted…

aipoch/medical-research-skills

Use this bioinformatics data analysis skill to construct a database-driven lncRNA-mRNA regulatory network from target lncRNA and/or gene lists by projecting shared miRNA evidence from local ceRNA…

aipoch/medical-research-skills

Differential gene expression analysis for bulk RNA-seq count matrices using a DESeq2-like workflow in Python; use when you need Wald tests, FDR correction, and optional LFC shrinkage for…

aipoch/medical-research-skills

Comprehensive tool for computational mass spectrometry using PyOpenMS; use when you need to read/write MS formats (mzML/mzXML/MGF), run signal processing (smoothing/peak picking), detect isotope…

aipoch/medical-research-skills

A skill your agent uses when estimating immune infiltration from bulk RNA-seq expression matrices with ssGSEA/GSVA, comparing case versus control groups, and generating downstream immune-score…

aipoch/medical-research-skills

A skill your agent uses when performing sample-level dimensionality reduction and visualization on abundance or OTU-style matrices with a companion group file, generating UMAP and/or t-SNE…

aipoch/medical-research-skills

A skill your agent uses when building a weighted gene co-expression network from a bulk expression matrix and a sample group file, filtering variable genes by MAD, identifying co-expression modules…

aipoch/medical-research-skills

Treats a ctDNA assay as a molecule-counting experiment at the Poisson edge and builds its analytical-validation case the measurement-science way.

GPTomics/bioSkills

Process many sequence files in batch (count, merge, split, convert, summarize) with memory-safe streaming and on-disk indexing using Biopython, pysam, or pyfastx.

GPTomics/bioSkills

Analyze codon usage and calculate CAI (Codon Adaptation Index), RSCU, and Nc with Biopython, and produce naive max-CAI codon-optimized sequences.

GPTomics/bioSkills

Read, write, and index compressed sequence files (gzip, bzip2, xz, BGZF) with Biopython and bgzip/samtools.

GPTomics/bioSkills

Generate consensus FASTA sequences by applying VCF variants onto a reference with bcftools consensus, or build viral/amplicon consensus with iVar.

GPTomics/bioSkills

Designs and analyzes combinatorial CRISPR screens covering paired-Cas9 (Big Papi, Najm 2018), enhanced AsCas12a multiplex (enCas12a, DeWeirdt 2021), in4mer 4-guide-array Cas12a (Esmaeili Anvar N et…

GPTomics/bioSkills

Analyzes CRISPR drug-modifier (chemogenomic) screens with drugZ (Colic et al.

GPTomics/bioSkills

Designs and analyzes pooled prime-editor (PE) screens for installing precise genetic variants without bystander confounding.

GPTomics/bioSkills

Designs genomics experiments so technical nuisance variation (batch, lane, plate, flow cell, operator, reagent lot, processing day) is balanced against the biological variable of interest and…

GPTomics/bioSkills

Controls error rates across thousands of simultaneous tests in genomics discovery using false-discovery-rate methods (Benjamini-Hochberg 1995; Benjamini-Yekutieli 2001 for arbitrary dependence…

GPTomics/bioSkills

Calculates statistical power for high-dimensional genomics experiments (bulk RNA-seq, scRNA-seq, ATAC-seq, ChIP-seq, methylation, proteomics) under negative-binomial count models using RNASeqPower…

GPTomics/bioSkills

Estimates the minimum biological replicates (or cells/events) for a target power at a target FDR in genomics experiments using ssizeRNA, PROPER, powsimR for scRNA-seq, and pilot-data dispersion…

GPTomics/bioSkills

Work with FASTQ quality scores using Biopython - access Phred scores, filter and trim by quality, compute per-position profiles, and convert between Sanger/Phred+33, Solexa, and Illumina/Phred+64…

GPTomics/bioSkills

Filter and select sequences by criteria (length, ID, GC content, N content, motifs, patterns, description) using Biopython, streaming so large files never load into RAM.

GPTomics/bioSkills

Reads, inspects, and writes Flow Cytometry Standard (FCS) files from conventional, spectral, and mass cytometry (CyTOF), and parses FlowJo/Cytobank/Diva workspaces.

GPTomics/bioSkills

Convert between sequence file formats (FASTA, FASTQ, GenBank, EMBL, Stockholm) and re-encode FASTQ quality offsets using Biopython Bio.SeqIO.

GPTomics/bioSkills

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/bioSkills

Call germline SNPs and indels with GATK HaplotypeCaller and the GVCF joint-genotyping workflow.

GPTomics/bioSkills

Build weighted gene co-expression networks to identify modules of co-regulated genes, relate them to phenotypes, and find hub genes using WGCNA, hdWGCNA, MEGENA, CEMiTool, and Gaussian graphical…

GPTomics/bioSkills

Infer gene regulatory networks from bulk or general expression data with mutual-information (ARACNe) and tree-ensemble (GENIE3, GRNBoost2) methods, and infer transcription-factor protein activity…

GPTomics/bioSkills

Build enhancer-driven gene regulatory networks (eGRNs) by integrating single-cell RNA-seq and ATAC-seq using SCENIC+, CellOracle base GRNs, Pando, FigR, DIRECT-NET, TRIPOD, and scMEGA.

GPTomics/bioSkills

Simulate transcription factor perturbation effects on cell state in silico with CellOracle and Dynamo, and predict transcriptional responses to genetic perturbations with GEARS, scGen, and CPA.

GPTomics/bioSkills

Infer transcription factor regulons from single-cell RNA-seq with pySCENIC by combining GRNBoost2 co-expression, cisTarget motif-enrichment pruning, and AUCell per-cell activity scoring.

GPTomics/bioSkills

Assesses the quality and completeness of a genome annotation with BUSCO (conserved single-copy ortholog recovery), OMArk (proteome completeness, consistency, and contamination), CheckM2 (prokaryotic…

GPTomics/bioSkills

Transfers gene annotations between genome assemblies via coordinate liftover (UCSC liftOver, CrossMap for same-species version updates) or feature/sequence projection (Liftoff for same/close…

GPTomics/bioSkills

Predicts protein-coding gene structures (exons, introns, UTRs) in eukaryotic genomes with BRAKER3 (RNA-seq + protein evidence), BRAKER1/BRAKER2, GALBA (protein-only), Funannotate (fungi), GeMoMa…

GPTomics/bioSkills

Assigns GO terms, Pfam/InterPro domains, KEGG orthologs, EC numbers, and product names to predicted proteins using eggNOG-mapper (orthology), InterProScan (domain signatures), and KofamScan (KEGG)…

GPTomics/bioSkills

Identifies non-coding RNAs (tRNA, rRNA, snoRNA, snRNA, riboswitches, sRNAs) using Infernal covariance-model search against Rfam, tRNAscan-SE 2.0 for tRNA, barrnap for rRNA, and ARAGORN for tmRNA…

GPTomics/bioSkills

Annotates bacterial and archaeal genomes (isolates, MAGs, plasmids) with Bakta (active versioned databases, NCBI-compliant output) or Prokka (legacy), producing GFF3/GenBank/EMBL/FASTA with INSDC…

GPTomics/bioSkills

Discovers, classifies, and masks repetitive elements and transposable elements with RepeatModeler2 (de novo family library), RepeatMasker (masking against a library), EDTA (plant/structural TEs), or…

GPTomics/bioSkills

Decides whether and how to polish a draft genome assembly to raise consensus accuracy (QV) with read-type-matched tools - Racon and medaka (ONT consensus), dorado polish, Polypolish and pypolca…

GPTomics/bioSkills