Results for “fastq”
12 skills
gabrielmoreira seq-wrangler
Runs NGS read QC, alignment, and BAM processing, wrapping FastQC, BWA/Bowtie2/Minimap2, SAMtools, and MultiQC for automated read-to-BAM workflows.
17 · bundle
gabrielmoreira bioqc-mcp
Automates sequencing quality control by running FastQC and MultiQC, extracting quality metrics, and generating publication-ready visualizations via a CLI or MCP stdio server.
17 · bundle
lingxling pysam
Read, write, and analyze genomic datasets including SAM/BAM/CRAM alignments, VCF/BCF variants, and FASTA/FASTQ sequences using a Pythonic interface to htslib.
253 · bundle
k-dense-ai pysam
Read, write, and manipulate genomic datasets including SAM/BAM/CRAM alignments, VCF/BCF variants, and FASTA/FASTQ sequences using a Pythonic interface to htslib.
30.2k · bundle
k-dense-ai bulk-rnaseq
Orchestrates a complete bulk RNA-seq differential-expression study from raw FASTQ reads through QC, alignment, quantification, differential expression, pathway enrichment, and publication figures.
30.2k · bundle
More results
gabrielmoreira wgs-prs
Takes raw whole-genome sequencing FASTQ files or a pre-existing VCF through variant calling, quality control, and polygenic risk score computation using the PGS Catalog.
17 · bundle
gabrielmoreira galaxy-bridge
Discovers and executes bioinformatics tools from the Galaxy ecosystem via natural language, with multi-signal scoring, workflow templates, and reproducibility bundles.
17 · bundle
antigravity jq
Query, filter, transform, and aggregate JSON data using jq in shell pipelines and scripts.
42.4k
gabrielmoreira flow-bio
Authenticate, browse pipelines, samples, and projects, upload data, launch pipeline executions, and check run status on any Flow.bio instance via CLI.
17 · bundle
k-dense-ai dnanexus-integration
Build and deploy apps/applets on the DNAnexus cloud genomics platform, manage data objects, run workflows, and use the dxpy Python SDK for genomics pipeline development and execution.
30.2k · bundle
k-dense-ai polars-bio
Perform high-performance genomic interval operations and bioinformatics file I/O on Polars DataFrames, including overlap, nearest, merge, coverage, complement, subtract, and reading/writing BED, VCF, BAM, GFF, FASTA, and FASTQ formats with streaming and cloud-native support.
30.2k · bundle
alterlab-ieu alterlab-geo
Access NCBI GEO (Gene Expression Omnibus) for gene expression and functional genomics data — search and download microarray and RNA-seq datasets by GSE, GSM, GPL, or GDS accession and retrieve SOFT, MINiML, and series matrix files. Use when locating public expression datasets, fetching processed expression matrices, downloading a study's supplementary files, or sourcing per-study transcriptomics data for differential-expression analysis. For raw FASTQ sequencing reads by SRA/ENA run accession use alterlab-ena; for reference tissue-expression baselines (median TPM across human tissues) use alterlab-gtex; for cancer cohort somatic mutations and copy-number use alterlab-cbioportal. Part of the AlterLab Academic Skills suite.
60 · bundle