BibiGPT CLI for summarizing videos, audio, and podcasts directly in the terminal. Use when the user wants to summarize a URL (YouTube, Bilibili, podcast, etc...
Analyze a BibTeX bibliography and generate a thematic tree diagram in Mermaid, plus a suggested article title (TARGET_TITLE). Stage 1 of the academic-pipeline.
A comprehensive Bilibili toolkit that integrates hot trending monitoring, video downloading, video watching/playback, subtitle downloading, and video publishing capabilities into…
Extract subtitles and transcripts from Bilibili and YouTube videos. Use when the user wants to get subtitles from B站 (Bilibili) or YouTube, extract Chinese/Japanese video…
Drafting deutsch-englischer Vertraege in Side-by-Side- oder Stacked-Layout. Bestimmt den Anwendungsfall (true bilingual, sovereign language, courtesy translation), waehlt das…
Russian language calibration for Billy Milligan agents. Load when session language is RU. Contains native speech patterns, swearing vocabulary, pet name styles, and anchor…
Annotate CLIP-seq binding sites to genomic features including 3'UTR, 5'UTR, CDS, introns, and ncRNAs. Use when characterizing where an RBP binds in transcripts.
Detect transcription factor binding sites through footprinting analysis in ATAC-seq data using TOBIAS.
Detect transcription factor binding footprints in ATAC-seq using TOBIAS, HINT-ATAC, Wellington, or scprinter.
Analyze transcription factor motif accessibility variability using chromVAR. Use when identifying which TF motifs show variable accessibility across samples or conditions in…
Bulk-query Ensembl BioMart (and other BioMart instances) for cross-database ID mapping, gene/transcript/exon coordinates, and ortholog tables.
Performs gene-level association from GWAS summary statistics via genetically predicted tissue expression using FUSION, PrediXcan, S-PrediXcan, S-MultiXcan, UTMOST, MOSTWAS, kTWAS,…
De novo motif discovery and known motif enrichment analysis using HOMER and MEME-ChIP. Identify transcription factor binding motifs in ChIP-seq, ATAC-seq, or other genomi — from…
Detects allele-specific transcription factor or histone modification binding from heterozygous-variant ChIP-seq using WASP (reference-bias filter; mandatory upstream), RASQUAL…
De novo motif discovery and known motif enrichment analysis using HOMER and MEME-ChIP. Identify transcription factor binding motifs in ChIP-seq, ATAC-seq, or other genomi — from…
ChIP-seq peak calling using MACS3 (or MACS2). Call narrow peaks for transcription factors or broad peaks for histone modifications.
Identifies super-enhancers from H3K27ac, MED1, or BRD4 ChIP-seq using ROSE, ROSE2, LILY, HOMER -style super, and ENCODE dELS cross-referencing.
Queries PharmGKB / CPIC / DPWG for drug-gene interactions; calls CYP2D6/CYP2C9/CYP2C19/DPYD/TPMT/NUDT15/UGT1A1/SLCO1B1 star alleles and phenotype with PharmCAT, Cyrius (CYP2D6…
Annotate CLIP-seq peaks or crosslink sites to RNA features (5'UTR, CDS, 3'UTR, intron, splice junction, snoRNA, tRNA, ncRNA, repeat elements) with ChIPseeker, RCAS, RBP-Maps (Yeo…
Infer integer allele-specific copy number, tumor purity, and ploidy from tumor sequencing by jointly modeling read depth (logR) and B-allele frequency (BAF) with ASCAT, Sequenza,…
Annotate CNVs with genes, pathways, and clinical significance. Use when interpreting CNV calls or identifying affected genes from copy number analysis.
Annotate copy number variant segments with overlapping genes, dosage-sensitivity scores, cancer driver databases, population frequencies, and clinical-variant content.
Visualize copy number profiles, segments, and compare across samples. Create publication-quality plots of CNV data from CNVkit, GATK, or other callers.
Visualize copy number profiles, segments, allele-specific tracks, and cohort patterns from CNVkit, GATK, ASCAT, FACETS, Sequenza, and other callers.
Detect copy number variants from targeted/exome sequencing using CNVkit. Supports tumor-normal pairs, tumor-only, and germline CNV calling.
Detect somatic and germline copy number variants from targeted, exome, and whole-genome sequencing with CNVkit, a read-depth caller that combines on-target and off-target…
Normalize read-depth copy-ratio profiles and segment them into copy-number regions using circular binary segmentation (CBS, DNAcopy), hidden Markov models, HaarSeg, and…
Resolve the architecture of focal oncogene amplifications — extrachromosomal DNA (ecDNA), breakage-fusion-bridge (BFB) cycles, homogeneously staining regions (HSR), and linear…
Call copy number variants using GATK best practices workflow. Supports both somatic (tumor-normal) and germline CNV detection from WGS or WES data.
Call copy number variants with the GATK best-practices workflows — the somatic CNV pipeline (CollectReadCounts, DenoiseReadCounts with tangent normalization, ModelSegments,…
Classify constitutional (germline) copy number variants for clinical reporting using the 2019 ACMG/ClinGen technical standards points-based framework, with ClassifyCNV an — from…
Quantify homologous recombination deficiency (HRD) from tumor copy number using the three genomic-scar metrics — loss of heterozygosity (LOH), large-scale state transitions (LST),…
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…
Resolve subclonal copy number, whole-genome doubling, and copy-number tumor evolution from bulk sequencing with Battenberg, TITAN, and MEDICC2.
Analyzes base editing and prime editing outcomes including editing efficiency, bystander edits, and indel frequencies.
Corrects the gene-independent copy-number artifact in CRISPR-Cas9 screens (Aguirre 2016 / Munoz 2016 Cancer Discov) where amplified loci appear essential from DNA-damage — from…
Designs pooled sgRNA libraries for CRISPR knockout, interference (CRISPRi), activation (CRISPRa), Cas12a multiplex, base-editor, and prime-editor screens.
Designs and analyzes pooled prime-editor (PE) screens for installing precise genetic variants without bystander confounding.
Quality control for pooled CRISPR screens covering library representation, Gini index, log-skew, replicate Pearson and Spearman concordance, essentialome precision-recall AUC…
Build sequence logos from aligned DNA, RNA, or protein motifs using ggseqlogo (R), Logomaker (Python), or WebLogo with explicit bits vs probability encoding, background-frequency…
Performs differential expression on bulk RNA-seq count data with edgeR's negative-binomial GLM and quasi-likelihood F-test framework.
Processes eDNA metabarcoding from raw paired-end reads to species tables, navigating ASV (DADA2, UNOISE3) vs OTU (swarm v2) decision (Callahan 2017 vs Schloss multi-copy-16S…
Query the Ensembl REST API for gene/transcript/protein lookup, sequence retrieval, comparative genomics (Compara), variant effect prediction (VEP), regulatory features, and…
Identifies differential m6A methylation between conditions from MeRIP-seq paired IP/input data using exomePeak2 with `bam_ip` + `bam_input` (control arm) and `bam_treated_ip` +…
Calls m6A peaks from MeRIP-seq / m6A-seq paired IP-vs-input data using exomePeak2 (transcript-aware, GC-bias-corrected Poisson GLM; Liu 2022 *NAR Genom Bioinform* 4:lqac046),…
Detects m6A modifications from Oxford Nanopore direct-RNA-sequencing (ONT DRS) signal data using m6Anet (Hendra 2022 *Nat Methods* 19:1590; multiple-instance-learning neural…
Aligns and QCs methylated-RNA-immunoprecipitation (MeRIP / m6A-seq) IP and input libraries using STAR or HISAT2 splice-aware mapping, samtools sort/index, IP/input matched-pair…
Visualises RNA-modification data with transcript-feature metagene plots (Guitar GuitarPlot with 5'UTR / CDS / 3'UTR scaling; MetaPlotR; deepTools `computeMatrix scale-regions`),…
Infer gene regulatory networks from bulk or general expression data with mutual-information (ARACNe) and tree-ensemble (GENIE3, GRNBoost2) methods, and infer transcription-factor…
Simulate transcription factor perturbation effects on cell state in silico with CellOracle and Dynamo, and predict transcriptional responses to genetic perturbations with GEARS,…
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…
Analyzes differential transcript usage (DTU) and isoform switches with functional consequence prediction (NMD via 50nt rule, ORF disruption, protein domain loss/gain, signal…
Analyze PacBio Iso-Seq data for full-length isoform discovery and quantification. Use when characterizing transcript diversity or identifying novel splice variants.
Analyze PacBio Iso-Seq data for full-length isoform discovery and quantification. Use when characterizing transcript diversity or identifying novel splice variants.
Analyzes alternative splicing from PacBio Iso-Seq (HiFi, Kinnex/MAS-Iso-seq) and Oxford Nanopore (direct cDNA, direct RNA, R10.4.1+) long-read RNA-seq with full-isoform…
Find patterns, motifs, and subsequences in biological sequences using Biopython. Use when searching for transcription factor binding sites, regulatory elements, or any se — from…
Post-translational modification analysis including phosphorylation, acetylation, and ubiquitination. Covers site localization, motif analysis, and quantitative PTM analys — from…
Post-translational modification analysis including phosphorylation, acetylation, and ubiquitination. Covers site localization, motif analysis, and quantitative PTM analys — from…
Align RNA-seq reads with STAR (Spliced Transcripts Alignment to a Reference). Supports two-pass mode for novel splice junction discovery.
Detect and quantify translated ORFs from Ribo-seq data including uORFs and novel ORFs using RiboCode and ORFquant.