GitHub
bio-single-cell-cell-annotation
Automated cell type annotation using reference-based methods including CellTypist, scPred, SingleR, and Azimuth for consistent, reproducible cell labeling.
☆ 300View skill
tools bioinformatics AI Skills
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GitHub
bio-de-visualization
Visualize differential expression results using DESeq2/edgeR built-in functions. Covers plotMA, plotDispEsts, plotCounts, plotBCV, sample distance heatmaps, and p-value histograms.
☆ 300View skill
GitHub
bio-metagenomics-metaphlan
Marker gene-based taxonomic profiling using MetaPhlAn 4. Provides accurate species-level relative abundances using clade-specific markers. Use when accurate taxonomic profiling is needed and computational resou...
☆ 300View skill
GitHub
bio-genome-assembly-long-read-assembly
De novo genome assembly from Oxford Nanopore or PacBio long reads using Flye and Canu. Produces highly contiguous assemblies suitable for complete bacterial genomes and resolving complex regions.
☆ 300View skill
GitHub
bio-restriction-sites
Find restriction enzyme cut sites in DNA sequences using Biopython Bio.Restriction. Search with single enzymes, batches of enzymes, or commercially available enzyme sets. Returns cut positions for linear or cir...
☆ 300View skill
GitHub
bio-genome-assembly-scaffolding
Scaffold contigs into chromosome-level assemblies using Hi-C data with YaHS, 3D-DNA, SALSA2, and validate with BUSCO and contact maps.
☆ 300View skill
GitHub
bio-genome-assembly-assembly-polishing
Polish genome assemblies to reduce errors using short reads (Pilon), long reads (Racon), or ONT-specific tools (medaka). Essential for improving long-read assembly accuracy.
☆ 300View skill
GitHub
bio-proteomics-peptide-identification
Peptide-spectrum matching and protein identification from MS/MS data. Covers database searching, spectral library matching, and FDR estimation using target-decoy approaches.
☆ 300View skill
GitHub
bio-write-sequences
Write biological sequences to files (FASTA, FASTQ, GenBank, EMBL) using Biopython Bio.SeqIO. Use when saving sequences, creating new sequence files, or outputting modified records.
☆ 300View skill
GitHub
bio-workflows-metagenomics-pipeline
End-to-end metagenomics workflow from FASTQ to taxonomic and functional profiles. Covers Kraken2 classification, Bracken abundance estimation, and HUMAnN functional profiling.
☆ 300View skill
GitHub
bio-proteomics-dia-analysis
Data-independent acquisition (DIA) proteomics analysis with DIA-NN and other tools. Covers library-free and library-based workflows for deep proteome profiling.
☆ 300View skill
GitHub
bio-crispr-screens-screen-qc
Quality control for pooled CRISPR screens. Covers library representation, read distribution, replicate correlation, and essential gene recovery. Use when assessing screen quality before hit calling or diagnosin...
☆ 300View skill
GitHub
bio-workflows-imc-pipeline
End-to-end imaging mass cytometry workflow from raw acquisitions to spatial cell analysis. Orchestrates image preprocessing, segmentation, phenotyping, and spatial statistics.
☆ 300View skill
GitHub
bio-spatial-transcriptomics-spatial-visualization
Visualize spatial transcriptomics data using Squidpy and Scanpy. Create tissue plots with gene expression, clusters, and annotations overlaid on histology images.
☆ 300View skill
GitHub
bio-workflows-scrnaseq-pipeline
End-to-end single-cell RNA-seq workflow from 10X Genomics data to annotated cell types. Covers QC, normalization, clustering, marker detection, and cell type annotation.
☆ 300View skill
GitHub
bio-read-qc-umi-processing
Extract, process, and deduplicate reads using Unique Molecular Identifiers (UMIs) with umi_tools. Use when library prep includes UMIs and accurate molecule counting is needed, such as in single-cell RNA-seq, lo...
☆ 300View skill
GitHub
bio-pathway-enrichment-visualization
Visualize enrichment results using enrichplot package functions. Covers dotplot, barplot, cnetplot, emapplot, gseaplot2, ridgeplot, and treeplot for clusterProfiler results.
☆ 300View skill
GitHub
bio-phylo-tree-io
Read, write, and convert phylogenetic tree files using Biopython Bio.Phylo. Use for parsing Newick, Nexus, PhyloXML, and NeXML tree formats, converting between formats, and handling multiple trees in a single f...
☆ 300View skill
GitHub
bio-workflows-longread-sv-pipeline
End-to-end workflow for detecting structural variants from long-read sequencing data. Covers ONT/PacBio alignment with minimap2 and SV calling with Sniffles or cuteSV.
☆ 300View skill
GitHub
bio-phasing-imputation-haplotype-phasing
Phase genotypes into haplotypes using Beagle or SHAPEIT. Resolves which alleles are inherited together on each chromosome. Use when preparing VCF files for imputation, HLA typing, or population genetic analyses...
☆ 300View skill
GitHub
bio-bedgraph-handling
Create, manipulate, and convert bedGraph files for genome browser visualization. Covers bedGraph format, conversion to/from bigWig, normalization, and signal processing. Use for handling coverage and signal tra...
☆ 300View skill
GitHub
bio-rna-quantification-featurecounts-counting
Count reads per gene from aligned BAM files using Subread featureCounts. Use when you have BAM files from STAR/HISAT2 and need gene-level counts for DESeq2/edgeR.
☆ 300View skill
GitHub
bio-expression-matrix-metadata-joins
Merge sample metadata with count matrices and add gene annotations. Use when preparing data for differential expression analysis or visualization.
☆ 300View skill
GitHub
bio-batch-processing
Process multiple sequence files in batch using Biopython. Use when working with many files, merging/splitting sequences, or automating file operations across directories.
☆ 300View skill
The default order uses GitHub repository stars from our indexed data. Stars belong to the source repository and may be shared by multiple skills. They indicate repository interest, not skill installs or an independent quality score.