GitHub
bio-consensus-sequences
Generate consensus FASTA sequences by applying VCF variants to a reference using bcftools consensus. Use when creating sample-specific reference sequences or reconstructing haplotypes.
☆ 300View skill
databases bioinformatics AI Skills
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GitHub
bio-pileup-generation
Generate pileup data for variant calling using samtools mpileup and pysam. Use when preparing data for variant calling, analyzing per-position read data, or calculating allele frequencies.
☆ 300View skill
GitHub
bio-read-qc-quality-filtering
Filter reads by quality scores, length, and N content using Trimmomatic and fastp. Apply sliding window trimming, remove low-quality bases from read ends, and discard reads below thresholds. Use when reads have...
☆ 300View skill
GitHub
bio-variant-calling-joint-calling
Joint genotype calling across multiple samples using GATK CombineGVCFs and GenotypeGVCFs. Essential for cohort studies, population genetics, and leveraging VQSR.
☆ 300View skill
GitHub
bio-phylo-tree-manipulation
Modify phylogenetic tree structure using Biopython Bio.Phylo. Use for rooting trees with outgroups or midpoint, pruning taxa, collapsing clades, ladderizing branches, and extracting subtrees.
☆ 300View skill
GitHub
bio-atac-seq-footprinting
Detect transcription factor binding sites through footprinting analysis in ATAC-seq data using TOBIAS. Use when identifying TF occupancy patterns within accessible regions, as TF binding protects DNA from Tn5 c...
☆ 300View skill
GitHub
bio-reverse-complement
Generate reverse complements and complements of DNA/RNA sequences using Biopython. Use when working with opposite strands, primer design, or converting between template and coding strands.
☆ 300View skill
GitHub
bio-spatial-transcriptomics-spatial-neighbors
Build spatial neighbor graphs for spatial transcriptomics data using Squidpy. Compute k-nearest neighbors, Delaunay triangulation, and radius-based connectivity for downstream spatial analyses.
☆ 300View skill
GitHub
bio-hi-c-analysis-hic-differential
Compare Hi-C contact matrices between conditions to identify differential chromatin interactions. Compute log2 fold changes, statistical significance, and visualize differential contact maps.
☆ 300View skill
GitHub
bio-workflows-somatic-variant-pipeline
End-to-end somatic variant calling from tumor-normal paired samples using Mutect2 or Strelka2. Covers preprocessing, variant calling, filtering, and annotation for cancer genomics.
☆ 300View skill
GitHub
bio-imaging-mass-cytometry-data-preprocessing
Load and preprocess imaging mass cytometry (IMC) and MIBI data. Covers MCD/TIFF handling, hot pixel removal, and image normalization. Use when starting IMC analysis from raw MCD files or preparing images for se...
☆ 300View skill
GitHub
bio-phasing-imputation-genotype-imputation
Impute missing genotypes using reference panels with Beagle or Minimac4. Use when increasing variant density for GWAS, harmonizing data across genotyping platforms, or inferring variants not directly typed in a...
☆ 300View skill
GitHub
bio-read-qc-adapter-trimming
Remove sequencing adapters from FASTQ files using Cutadapt and Trimmomatic. Supports single-end and paired-end reads, Illumina TruSeq, Nextera, and custom adapter sequences. Use when FastQC shows adapter contam...
☆ 300View skill
GitHub
bio-long-read-sequencing-clair3-variants
Deep learning-based variant calling from long reads using Clair3 for SNPs and small indels. Use when calling germline variants from ONT or PacBio alignments, particularly when high accuracy is needed for clinic...
☆ 300View skill
GitHub
bio-vcf-statistics
Generate variant statistics, sample concordance, and quality metrics using bcftools stats and gtcheck. Use when evaluating variant quality, comparing samples, or summarizing VCF contents.
☆ 300View skill
GitHub
bio-duplicate-handling
Mark and remove PCR/optical duplicates using samtools fixmate and markdup. Use when preparing alignments for variant calling or when duplicate reads would bias analysis.
☆ 300View skill
GitHub
bio-gatk-variant-calling
Variant calling with GATK HaplotypeCaller following best practices. Covers germline SNP/indel calling, GVCF workflow for cohorts, joint genotyping, and variant quality score recalibration (VQSR). Use for produc...
☆ 300View skill
GitHub
bio-metagenomics-abundance
Species abundance estimation using Bracken with Kraken2 output. Redistributes reads from higher taxonomic levels to species for more accurate estimates. Use when accurate species-level abundances are needed fro...
☆ 300View skill
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
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
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