GitHub
bio-compressed-files
Read and write compressed sequence files (gzip, bzip2, BGZF) using Biopython. Use when working with .gz or .bz2 sequence files. Use BGZF for indexable compressed files.
☆ 300View skill
Databases AI Skills
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GitHub
bio-flow-cytometry-compensation-transformation
Spillover compensation and data transformation for flow cytometry. Covers compensation matrix calculation, application, and biexponential/arcsinh transforms. Use when correcting spectral overlap between fluorop...
☆ 300View skill
GitHub
bio-population-genetics-population-structure
Analyze population structure using PCA and admixture analysis with PLINK and ADMIXTURE. Identify population clusters, assess ancestry proportions, visualize genetic structure, and choose optimal K for admixture...
☆ 300View skill
GitHub
bio-vcf-basics
View, query, and understand VCF/BCF variant files using bcftools and cyvcf2. Use when inspecting variants, extracting specific fields, or understanding VCF format structure.
☆ 300View skill
GitHub
bio-single-cell-batch-integration
Integrate multiple scRNA-seq samples/batches using Harmony, scVI, Seurat anchors, and fastMNN. Remove technical variation while preserving biological differences.
☆ 300View skill
GitHub
bio-microbiome-diversity-analysis
Alpha and beta diversity analysis for microbiome data. Calculate within-sample richness, evenness, and between-sample dissimilarity with phyloseq and vegan. Use when comparing community composition across sampl...
☆ 300View skill
GitHub
bio-chipseq-qc
ChIP-seq quality control metrics including FRiP (Fraction of Reads in Peaks), cross-correlation analysis (NSC/RSC), library complexity, and IDR (Irreproducibility Discovery Rate) for replicate concordance. Use...
☆ 300View skill
GitHub
bio-rna-quantification-count-matrix-qc
Quality control and exploration of RNA-seq count matrices before differential expression. Check for outliers, batch effects, and sample relationships.
☆ 300View skill
GitHub
bio-longread-structural-variants
Detect structural variants from long-read alignments using Sniffles, cuteSV, and SVIM. Use when detecting deletions, insertions, inversions, translocations, or complex rearrangements from ONT or PacBio data, es...
☆ 300View skill
GitHub
bio-alignment-io
Read, write, and convert multiple sequence alignment files using Biopython Bio.AlignIO. Supports Clustal, PHYLIP, Stockholm, FASTA, Nexus, and other alignment formats for phylogenetics and conservation analysis...
☆ 300View skill
GitHub
bio-single-cell-scatac-analysis
Single-cell ATAC-seq analysis with Signac (R/Seurat) and ArchR. Process 10X Genomics scATAC data, perform QC, dimensionality reduction, clustering, peak calling, and motif activity scoring with chromVAR.
☆ 300View skill
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
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
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