Source

jaechang-hits/sciagent-skills

208 skills · 12K combined installs

Skills from this source

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Skill
Source
8W Activity
Installs
1
clinpgx-database Query the ClinPGx (formerly PharmGKB) REST API plus the CPIC PostgREST companion API for pharmacogenomic clinical ann…
jaechang-hits/sciagent-skills
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2
deseq2-differential-expression Bulk RNA-seq DE with R/Bioconductor DESeq2. Negative binomial GLM, empirical Bayes shrinkage, Wald/LRT tests, multi-f…
jaechang-hits/sciagent-skills
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3
gene-database NCBI Gene via E-utilities: curated records across 1M+ taxa. Official symbols, aliases, RefSeq IDs, summaries, coordin…
jaechang-hits/sciagent-skills
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4
samtools-bam-processing CLI toolkit for SAM/BAM/CRAM: sort, index, convert, filter, QC alignments. Core commands: view, sort, index, flagstat…
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5
bedtools-genomic-intervals Genomic interval ops on BED/BAM/GFF/VCF. Find overlaps, merge intervals, compute coverage, extract FASTA, find neares…
jaechang-hits/sciagent-skills
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6
celltypist-cell-annotation Automated scRNA-seq cell type annotation via pre-trained logistic regression. 45+ models: immune, gut, lung, brain, f…
jaechang-hits/sciagent-skills
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7
cosmic-database Query COSMIC for cancer somatic mutations, gene census, mutational signatures, drug resistance variants. REST API v3.…
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8
dbsnp-database Query NCBI dbSNP for SNP records by rsID, gene, or region via E-utilities and Variation Services REST API. Retrieve a…
jaechang-hits/sciagent-skills
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ensembl-database Ensembl REST API for gene/transcript/variant annotations in 300+ species. Gene info by symbol/ID, sequence, cross-ref…
jaechang-hits/sciagent-skills
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10
geo-database NCBI GEO access via GEOparse and E-utilities. Search by keyword/organism/platform, download GSE series matrices, pars…
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gget-genomic-databases Unified CLI/Python interface to 20+ genomic databases. Gene lookups (Ensembl search/info/seq), BLAST/BLAT, AlphaFold,…
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12
gseapy-gene-enrichment GSEA and over-representation analysis (ORA) for RNA-seq and proteomics. Wraps Enrichr for ORA against MSigDB, KEGG, G…
jaechang-hits/sciagent-skills
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13
gwas-database NHGRI-EBI GWAS Catalog REST API for SNP-trait associations from published GWAS. Query studies, associations, variants…
jaechang-hits/sciagent-skills
35
14
harmony-batch-correction Harmony batch correction for scRNA-seq and other omics. Removes batch effects from PCA embeddings while preserving bi…
jaechang-hits/sciagent-skills
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kegg-database KEGG REST API (academic only). Pathways, genes, compounds, enzymes, diseases, drugs via 7 ops (info/list/find/get/con…
jaechang-hits/sciagent-skills
35
16
monarch-database Monarch Initiative knowledge graph REST API for disease-gene-phenotype associations and cross-species orthology. MOND…
jaechang-hits/sciagent-skills
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multiqc-qc-reports Aggregates QC from 150+ bioinformatics tools into one interactive HTML report. Scans FastQC, samtools, STAR, HISAT2, …
jaechang-hits/sciagent-skills
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single-cell-annotation-guide Decision framework for manual marker-based, automated (CellTypist), and reference-based (popV) cell type annotation i…
jaechang-hits/sciagent-skills
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19
vcf-variant-filtering Guide to quality filtering raw VCF files before computing summary stats (Ts/Tv ratio, variant counts, AF distribution…
jaechang-hits/sciagent-skills
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20
anndata-data-structure Annotated matrices for single-cell genomics. Stores X with obs/var metadata, layers, embeddings (obsm/varm), graphs (…
jaechang-hits/sciagent-skills
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21
bioservices-multi-database Unified Python interface to 40+ bioinformatics web services: UniProt proteins, KEGG pathways, ChEMBL/ChEBI/PubChem, B…
jaechang-hits/sciagent-skills
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22
busco-status-interpretation Guide to interpreting BUSCO completeness statuses: why Duplicated BUSCOs count as complete, parsing output files, com…
jaechang-hits/sciagent-skills
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23
cbioportal-database Cancer genomics (TCGA et al.) via cBioPortal REST API. Retrieve somatic mutations, CNAs, expression, clinical data (s…
jaechang-hits/sciagent-skills
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24
cellxgene-census Query CELLxGENE Census (61M+ cells). Search by cell type/tissue/disease/organism; get AnnData, stream out-of-core, tr…
jaechang-hits/sciagent-skills
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25
clinvar-database Query NCBI ClinVar via E-utilities for variant clinical significance, pathogenicity, disease associations. Search by …
jaechang-hits/sciagent-skills
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cnvkit-copy-number Detect somatic CNVs from WES/WGS/targeted BAMs (CNVkit v0.9.x). Bin coverage in target/antitarget regions, normalize …
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27
deeptools-ngs-analysis NGS CLI for ChIP/RNA/ATAC-seq. BAM→bigWig with RPGC/CPM/RPKM, sample correlation/PCA, heatmaps/profiles around featur…
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ena-database ENA REST API for sequences, reads, assemblies, and annotations. Portal API search, Browser API retrieval (XML/FASTA/E…
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encode-database ENCODE Portal REST API for regulatory genomics: TF ChIP-seq, ATAC-seq/DNase-seq peaks, histone marks, and RNA-seq acr…
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featurecounts-rna-counting Counts RNA-seq reads overlapping GTF gene features. Takes sorted STAR BAMs plus GTF; outputs a per-gene tab-delimited…
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geniml Python library for genomic interval ML. Train/apply region2vec embeddings turning BED regions into vectors, index int…
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gnomad-database gnomAD v4 population variant frequencies via GraphQL API. Allele counts and frequencies stratified by ancestry (AFR, …
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gtars Rust-backed Python library for fast genomic token arithmetic and BED processing. High-performance BED I/O, interval s…
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jaspar-database JASPAR 2024 TF binding profiles via REST API and pyJASPAR. Retrieve PFMs/PWMs by TF name, JASPAR ID, species, or stru…
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mouse-phenome-database Retrieve mouse phenotype data from the Jackson Laboratory Mouse Phenome Database (MPD) via its REST API. Browse 520+ …
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popv-cell-annotation Consensus cell type annotation: runs 10+ algorithms (KNN-Harmony/BBKNN/Scanorama/scVI, CellTypist, ONCLASS, Random Fo…
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prokka-genome-annotation Annotate prokaryotic genomes (bacteria, archaea, viruses) via Prokka's BLAST/HMM pipeline. Identifies CDS, rRNA, tRNA…
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pysam-genomic-files Read/write SAM/BAM/CRAM, VCF/BCF, FASTA/FASTQ. Region queries, pileup, variant filtering, read groups. Python htslib …
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quickgo-database Query EBI QuickGO REST API for GO terms and protein annotations. Fetch term metadata by ID, search by keyword, walk a…
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regulomedb-database Query RegulomeDB v2 GET REST API to score variants for regulatory function and retrieve overlapping evidence (TF bind…
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remap-database Query ReMap 2022 TF ChIP-seq peak database via REST API and BED downloads. Retrieve TF peaks overlapping a region (ch…
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salmon-rna-quantification Ultra-fast RNA-seq transcript/gene quantification via quasi-mapping (no BAM). Builds a k-mer index from transcriptome…
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scvi-tools-single-cell Deep generative models for single-cell omics: probabilistic batch correction (scVI), semi-supervised annotation (scAN…
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star-rna-seq-aligner Splice-aware RNA-seq aligner producing sorted BAM and splice junction tables. Builds genome index, runs two-pass alig…
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ucsc-genome-browser Query UCSC Genome Browser REST API for DNA sequences, tracks, gene models, and conservation across 100+ assemblies. R…
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depmap-crispr-essentiality DepMap CRISPR gene effect (Chronos) analysis: sign convention for essentiality, per-gene NaN-safe Spearman correlatio…
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bakta-genome-annotation Annotate bacterial and archaeal genomes and plasmids with Bakta's Prodigal/HMM/diamond pipeline. Identifies CDS, ncRN…
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roary-pangenome Compute the bacterial pan-genome from Prokka/Bakta GFF3 annotations with Roary's CD-HIT + BLAST + MCL clustering pipe…
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opentrons-integration Opentrons Protocol API v2 for OT-2/Flex: Python protocols for pipetting, serial dilutions, PCR, plate replication; co…
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plotly-interactive-visualization Interactive visualization with Plotly. 40+ chart types (scatter, line, heatmap, 3D, geographic) with hover, zoom, pan…
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