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bio-workflows-genome-assembly-pipeline
Complete workflow from sequencing reads to polished, quality-assessed genome assembly. Reads (short and/or long) [1. QC & Filtering] -----> fastp, Nan...
bio-workflows-gwas-pipeline
Complete workflow for genome-wide association studies from genotype data to significant associations. VCF/PLINK files [1. QC Filtering] ------> Sample...
bio-workflows-hic-pipeline
Complete workflow for Hi-C chromosome conformation capture analysis. Hi-C FASTQ files [1. Alignment & Pairs] --> bwa-mem2 + pairtools [2. Matrix Gener...
bio-workflows-metabolomics-pipeline
Raw MS Data (mzML/mzXML) ──> Peak Detection ──> Feature Matrix ┌─────────────────────────────────────────────┐ │ metabolomics-pipeline ...
bio-workflows-metagenomics-pipeline
Complete workflow from metagenomic FASTQ to taxonomic and functional profiles. FASTQ files [1. QC & Host Removal] --> fastp + Bowtie2 [2. Taxonomic Cl...
bio-workflows-multiome-pipeline
Complete workflow for 10X Multiome (joint scRNA + scATAC) analysis using Seurat and Signac. 10X Multiome data [1. Load Data] ---------> Read RNA + ATA...
bio-workflows-outbreak-pipeline
Complete workflow for genomic epidemiology: from pathogen isolates to transmission networks and outbreak characterization. Pathogen Isolate Genomes (F...
bio-workflows-proteomics-pipeline
Raw MS Data (mzML) ──> MaxQuant/DIA-NN ──> proteinGroups.txt ┌────────────────────────────────────────────┐ │ proteomics-pipeline ...
bio-workflows-riboseq-pipeline
FASTQ → Preprocessing → rRNA removal → Alignment → P-site → TE → ORF calling cutadapt -a CTGTAGGCACCATCAAT \ --minimum-length 25 --maximum-length 35 \...
bio-workflows-somatic-variant-pipeline
Complete workflow for calling somatic mutations from tumor-normal paired samples. Tumor BAM + Normal BAM ├── Preprocessing (if needed) │ └── MarkDup...
bio-workflows-spatial-pipeline
Complete workflow for analyzing Visium, Xenium, or other spatial transcriptomics data. Spatial data (Space Ranger output) [1. Load Data] ---------> Re...
bio-workflows-tcr-pipeline
FASTQ → MiXCR align → Assemble → Export → VDJtools diversity → Visualization mixcr align -s hsa -p rna-seq \ R1.fastq.gz R2.fastq.gz \ aligned.vdjca m...