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SkillsMP has collected 213 skills from Pavel-Kravchenko/Bioinformatics. Open a skill to review its source and details.
Pavel-Kravchenko/BioinformaticsShowing 40 of 213 collected skills.
Assign SARS-CoV-2 Pango lineages with Pangolin/Nextclade and deconvolve wastewater into lineage fractions with Freyja (variants/demix). Use when doing variant surveillance, wastewater epidemiology, lineage tracking, or VOC/VOI classification.
Compute TCR/BCR clonotype diversity (Shannon, Simpson, clonality, Chao1, D50) from AIRR/10x VDJ tables; explains IMGT V/D/J nomenclature and CDR3 junctions. Use for repertoire diversity, clonal expansion, or scTCR-seq analysis.
Assemble viral genomes from ARTIC amplicon FASTQ with minimap2/iVar/LoFreq; call consensus, detect quasispecies variants. Use when doing SARS-CoV-2/HIV/Influenza assembly, ARTIC pipelines, or minority variant calling.
Dock ligand libraries with AutoDock Vina/meeko, filter hits by ADMET (Lipinski, LogS, hERG), rank by composite docking+QSAR score in pandas. Use when docking SMILES/SDF vs a target or prioritizing virtual screening hits.
Align WGBS/RRBS bisulfite FASTQ with Bismark, extract per-CpG methylation into beta/M-values. Use for bismark_genome_preparation, deduplicate_bismark, bismark_methylation_extractor, or bismark.cov/CpG_report analysis.
Write Snakemake rules/wildcards/config and Nextflow DSL2 processes/channels; run nf-core pipelines (rnaseq, sarek) on SLURM/AWS/GCP. Use when building a Snakefile, DSL2 workflow, or nf-core samplesheet.
Fetch sequences via NCBI Entrez (esearch/efetch/elink), UniProt REST, and RCSB PDB APIs with BioPython/urllib. Use when picking a database, decoding accession prefixes (NM_/XM_/GSE/SRR), or cross-linking a gene NCBI-UniProt-PDB.
Manipulate Seq/SeqRecord objects, parse FASTA/FASTQ/GenBank with SeqIO, query NCBI via Entrez, and run PairwiseAligner in Biopython. Use for sequence I/O, translation, reverse complement, GC content, or NCBI fetch in Python.
Search protein/nucleotide sequences for homologs with NCBI BLAST+ (blastp/blastn/blastx/tblastn) via Biopython qblast or a local blastdb; parse E-value/bit-score/identity. Use for BLAST search, homology/similarity search, or FASTA annotation.
Parse Sanger .ab1/.abi chromatograms with BioPython, extract Phred quality/trace channels, plot traces, quality-trim, and flag het double-peaks. Use for .ab1/.scf files or detecting het SNPs/mixed peaks.
Build dot plots, detect synteny/rearrangements, classify orthologs vs paralogs, compute pan-genomes; pick MUMmer/LASTZ/minimap2 for alignment. Use when comparing genomes, reading a dot plot, or finding synteny/orthologs.
Translate DNA per-frame, score codon usage bias (RSCU/CAI), simulate restriction digests/ORFs, and test three-point-cross mapping and Hardy-Weinberg equilibrium. Use for CAI, virtual digests, crossover mapping, or HWE tests.
Build/scan PWMs (PPM, log-odds, info content, logos) for DNA motifs, convert PROSITE patterns to regex, parse HMMER domtblout/Pfam hits. Use for TF binding scans, promoter motifs, PROSITE matches, or Pfam/InterPro domain mapping.
Decode GO evidence codes (IDA/IEA/TAS), propagate GO annotations via the true path rule, and run ORA (hypergeometric test + BH-FDR) in Python/R. Use when doing GO enrichment, evidence-code checks, or DAG annotation propagation.
Analyze Hi-C contact matrices with cooler/cooltools: load .cool/.mcool files, visualize contact maps, compute P(s) decay curves, call A/B compartments (eigenvector), detect TAD boundaries (insulation score), and build pileups. Use when working with Hi-C data,…
Build PFM/PPM/PWM from TF binding sites, score/scan DNA with NumPy, pick thresholds, test motif enrichment (Fisher/BH-FDR). Use for ChIP-seq/SELEX motif scoring, IUPAC consensus, or JASPAR/HOCOMOCO matching.
Align FASTA sequences via MAFFT/MUSCLE/Clustal Omega, parse with Biopython AlignIO, build UPGMA guide trees, score sum-of-pairs/consensus/conservation. Use for MSA, MSA tool choice, consensus/logo, or guide-tree building.
Compute DNA helix geometry (A/B/Z-DNA), nearest-neighbor duplex free energy (SantaLucia), and RNA dot-bracket structure/Nussinov folding with Biopython. Use when analyzing helix groove geometry, oligo Tm/stability, or RNA stem-loop/hairpin structure.
Align two protein/DNA sequences with Biopython's PairwiseAligner (global Needleman-Wunsch, local Smith-Waterman), BLOSUM/PAM substitution matrices, and affine gap penalties; compute percent identity/similarity and E-values. Use when doing pairwise sequence…
Run GO/KEGG pathway enrichment via ORA (hypergeometric test) or GSEA, with BH-FDR and KEGG REST API queries. Use for "GO enrichment", "GSEA", "ORA vs GSEA", or "pathway enrichment" requests.
Build NJ/UPGMA trees from aligned FASTA with BioPython Bio.Phylo, score p-distance/JC69/K2P models, and parse Newick with bootstrap support. Use for tree building from an MSA, Newick I/O, or bootstrap-value interpretation.
Parse PDB files with BioPython Bio.PDB, compute distance/angle/dihedral/RMSD, superimpose structures (Kabsch), assign DSSP secondary structure. Use for protein structure analysis, RMSD/alignment, contact maps, Ramachandran plots.
Build PFM/PPM/PWM matrices from aligned sites with NumPy, scan sequences on both strands, compute information content, plot sequence logos, convert PROSITE patterns to regex. Use for motif scanning, TF binding site scoring, or PROSITE-to-regex tasks.
Build reproducible, resumable bioinformatics pipelines with Snakemake rules or Nextflow DSL2 processes, run nf-core pipelines, and add pytest unit tests plus GitHub Actions CI. Use when writing a Snakefile, defining Nextflow processes/channels, scaling a…
Fetch sequences from NCBI Entrez/UniProt/PDB/Ensembl REST APIs via BioPython SeqIO; read/write FASTA/GenBank/FASTQ. Use when downloading by accession/gene name, batch-fetching records, or converting sequence file formats.
Parse SMILES/SDF with RDKit, build ChEMBL QSAR models, dock ligands with AutoDock Vina, predict ADMET/Lipinski properties. Use for compound screening, Tanimoto similarity, Rule of Five filtering.
Align/call ChIP-seq peaks with Bowtie2+MACS3, run DiffBind binding and ChIPseeker annotation in R, visualize with deepTools. Use for TF/histone peak calling, narrow vs broad peaks, FRiP/NSC/RSC QC, or peak annotation.
Classify variants via ACMG/AMP + CADD/REVEL/SpliceAI; dock ligands with AutoDock Vina; set up GROMACS MD; run Scanpy scRNA-seq QC/clustering. Use for variant classification, docking, MD setup, or scRNA-seq.
Align WGBS/RRBS bisulfite reads with Bismark; call DMRs/DMPs with methylKit or BSmooth. Use when analyzing bisulfite sequencing, CpG beta values, .cov/cytosine_report files, or DNAm epigenetic age (Horvath/GrimAge).
Retrieve PDF/image pages with ColPali late-interaction embeddings and answer questions via Qwen2-VL/LLaVA. Use when doing document RAG, PDF QA, or retrieval over scanned papers/reports.
Write robust Bash scripts to batch-process FASTQ/BAM/VCF/FASTA files: variables, set -euo pipefail error handling, loops over sample sheets, functions, traps, and awk/sed text processing. Use when automating a multi-sample pipeline, writing a shell wrapper…
Run t-test/Mann-Whitney/ANOVA/chi-square tests, BH-FDR correction, and power analysis in SciPy, statsmodels, R. Use when comparing groups, interpreting p-values/CIs, correcting many gene-level tests, or sizing an experiment.
Fix UTF-8/Latin-1/CP1251 decode errors, strip BOM, repair mojibake, normalize CRLF endings, remove hidden Unicode in FASTA/GFF text. Use when hitting UnicodeDecodeError or garbled text from Windows/Excel exports.
Version-control bioinformatics scripts with git init/add/commit/branch/merge/stash/tag and .gitignore for FASTQ/BAM/VCF. Use when setting up a repo, undoing a commit, or resolving a merge conflict.
Linux CLI basics: cp/mv/rm, grep/awk/find, pipes, chmod, gzip/tar, wget/scp/rsync, ps/kill. Use when writing a bash pipeline, inspecting FASTA/FASTQ/BAM/BED/VCF on a server, or filtering lines with grep/awk.
Model bioinformatics data with probability distributions (Normal, Binomial, Poisson, Negative Binomial) using scipy.stats — compute PMF/PDF/CDF/SF/PPF, simulate variant allele counts, mutation rates, and RNA-seq overdispersion. Use when doing probability…
Read/write R syntax for bioinformatics (vectors, data.frame, matrices, d/p/q/r distributions, DESeq2). Use when porting Python to R, debugging R from a paper/pipeline, or running DESeq2/edgeR/Seurat scripts.
Run exact/nonparametric hypothesis tests in R: binom.test, sign test, wilcox.test/wilcox.exact (Wilcoxon signed-rank and Mann-Whitney U), kruskal.test with Dunn post-hoc, Hodges-Lehmann CIs, and binomial power/sample-size functions. Use when a user asks to…
Fit/diagnose R lm() regression and compute Pearson/Spearman/Kendall correlation with Fisher z CIs. Use for lm() regression, residual diagnostics, correlation CIs, or t.test/shapiro.test checks.
Run scipy.stats/statsmodels tests (t-test, Mann-Whitney, ANOVA, chi-square, Fisher's exact, Pearson/Spearman) on expression/count/genotype data. Use when comparing groups, correcting p-values (FDR), or computing power/sample size in Python.