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
databases bioinformatics AI Skills
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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
GitHub
bio-metagenomics-visualization
Visualize metagenomic profiles using R (phyloseq, microbiome) and Python (matplotlib, seaborn). Create stacked bar plots, heatmaps, PCA plots, and diversity analyses. Use when creating publication-quality figur...
☆ 300View skill
GitHub
bio-paired-end-fastq
Handle paired-end FASTQ files (R1/R2) using Biopython. Use when working with Illumina paired reads, synchronizing pairs, interleaving/deinterleaving, or filtering paired data.
☆ 300View skill
GitHub
bio-workflows-spatial-pipeline
End-to-end spatial transcriptomics workflow for Visium/Xenium data. Covers data loading, preprocessing, spatial analysis, domain detection, and visualization with Squidpy.
☆ 300View skill
GitHub
bio-genome-intervals-bigwig-tracks
Create and read bigWig browser tracks for visualizing continuous genomic data. Convert bedGraph to bigWig, extract signal values, and generate coverage tracks using UCSC tools and pyBigWig. Use when preparing c...
☆ 300View skill
GitHub
bio-single-cell-cell-communication
Infer cell-cell communication networks from scRNA-seq data using CellChat, NicheNet, and LIANA for ligand-receptor interaction analysis.
☆ 300View skill
GitHub
bio-vcf-manipulation
Merge, concatenate, sort, intersect, and subset VCF files using bcftools. Use when combining variant files, comparing call sets, or restructuring VCF data.
☆ 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.