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.
☆ 300查看技能
工具与集成 AI 技能
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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.
☆ 300查看技能
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...
☆ 300查看技能
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...
☆ 300查看技能
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...
☆ 300查看技能
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...
☆ 300查看技能
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.
☆ 300查看技能
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.
☆ 300查看技能
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...
☆ 300查看技能
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...
☆ 300查看技能
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.
☆ 300查看技能
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.
☆ 300查看技能
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...
☆ 300查看技能
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.
☆ 300查看技能
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...
☆ 300查看技能
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.
☆ 300查看技能
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.
☆ 300查看技能
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.
☆ 300查看技能
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.
☆ 300查看技能
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.
☆ 300查看技能
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.
☆ 300查看技能
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...
☆ 300查看技能
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.
☆ 300查看技能
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.
☆ 300查看技能
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