GitHub
bio-read-alignment-bowtie2-alignment
Align short reads using Bowtie2 with local or end-to-end modes. Use for ChIP-seq, ATAC-seq, or when you need flexible alignment modes. Supports gapped alignment.
☆ 300查看技能
databases bioinformatics AI 技能
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GitHub
bio-microbiome-taxonomy-assignment
Taxonomic classification of ASVs using reference databases like SILVA, GTDB, or UNITE. Covers naive Bayes classifiers (DADA2, IDTAXA) and exact matching approaches. Use when assigning taxonomy to ASVs after DAD...
☆ 300查看技能
GitHub
bio-atac-seq-nucleosome-positioning
Extract nucleosome positions from ATAC-seq data using NucleoATAC, ATACseqQC, and fragment analysis. Use when analyzing chromatin organization, identifying nucleosome-free regions at promoters, or characterizing...
☆ 300查看技能
GitHub
bio-differential-expression-timeseries-de
Analyze time-series RNA-seq data using limma voom with splines, maSigPro, and ImpulseDE2. Identify genes with dynamic expression patterns.
☆ 300查看技能
GitHub
bio-proteomics-proteomics-qc
Quality control and assessment for proteomics data. Covers sample quality metrics, missing value patterns, replicate correlation, batch effect detection, and intensity distribution checks.
☆ 300查看技能
GitHub
bio-crispr-batch-correction
Batch effect correction for CRISPR screens. Covers normalization across batches, technical replicate handling, and batch-aware analysis. Use when combining screens from multiple batches or correcting systematic...
☆ 300查看技能
GitHub
bio-workflows-atacseq-pipeline
End-to-end ATAC-seq workflow from FASTQ files to differential accessibility and TF footprinting. Covers alignment, peak calling with MACS3, QC metrics, and optional TOBIAS footprinting.
☆ 300查看技能
GitHub
bio-multi-omics-mixomics-analysis
Supervised and unsupervised multi-omics integration with mixOmics. Includes sPLS for pairwise integration and DIABLO for multi-block discriminant analysis.
☆ 300查看技能
GitHub
bio-population-genetics-association-testing
Genome-wide association studies (GWAS) with PLINK. Perform case-control and quantitative trait association testing using logistic/linear regression with covariates, generate Manhattan and QQ plots for result vi...
☆ 300查看技能
GitHub
bio-phasing-imputation-imputation-qc
Quality control of phasing and imputation results. Filter by INFO scores, assess accuracy, and prepare imputed data for downstream analysis. Use when filtering low-quality imputed variants or validating imputat...
☆ 300查看技能
GitHub
bio-variant-calling
Call SNPs and indels from aligned reads using bcftools mpileup and call. Use when detecting variants from BAM files or generating VCF from alignments.
☆ 300查看技能
GitHub
bio-workflows-multi-omics-pipeline
End-to-end multi-omics integration workflow. Orchestrates data harmonization, MOFA/mixOmics integration, factor interpretation, and downstream analysis across transcriptomics, proteomics, metabolomics, and othe...
☆ 300查看技能
GitHub
bio-rna-quantification-tximport-workflow
Import transcript-level quantifications from Salmon/kallisto into R for gene-level analysis with DESeq2/edgeR using tximport or tximeta.
☆ 300查看技能
GitHub
bio-flow-cytometry-clustering-phenotyping
Unsupervised clustering and cell type identification for flow/mass cytometry. Covers FlowSOM, Phenograph, and CATALYST workflows. Use when discovering cell populations in high-dimensional cytometry data without...
☆ 300查看技能
GitHub
bio-alignment-statistics
Generate alignment statistics using samtools flagstat, stats, depth, and coverage. Use when assessing alignment quality, calculating coverage, or generating QC reports.
☆ 300查看技能
GitHub
bio-longread-medaka
Polish assemblies and call variants from Oxford Nanopore data using medaka. Uses neural networks trained on specific basecaller versions. Use when improving ONT-only assemblies or calling variants from Nanopore...
☆ 300查看技能
GitHub
bio-phasing-imputation-reference-panels
Download, prepare, and manage reference panels for phasing and imputation. Covers 1000 Genomes, HRC, and TOPMed panels. Use when setting up imputation infrastructure or selecting appropriate reference panels fo...
☆ 300查看技能
GitHub
bio-read-qc-fastp-workflow
All-in-one read preprocessing with fastp including adapter trimming, quality filtering, deduplication, base correction, and HTML report generation. Use when preprocessing Illumina data and wanting a single fast...
☆ 300查看技能
GitHub
bio-alignment-filtering
Filter alignments by flags, mapping quality, and regions using samtools view and pysam. Use when extracting specific reads, removing low-quality alignments, or subsetting to target regions.
☆ 300查看技能
GitHub
bio-reference-operations
Generate consensus sequences and manage reference files using samtools. Use when creating consensus from alignments, indexing references, or creating sequence dictionaries.
☆ 300查看技能
GitHub
bio-imc-interactive-annotation
Interactive cell type annotation for IMC data. Covers napari-based annotation, marker-guided labeling, training data generation, and annotation validation. Use when manually annotating cell types for training c...
☆ 300查看技能
GitHub
bio-workflows-chipseq-pipeline
End-to-end ChIP-seq workflow from FASTQ files to annotated peaks. Covers QC, alignment, peak calling with MACS3, and peak annotation with ChIPseeker.
☆ 300查看技能
GitHub
bio-single-cell-trajectory-inference
Infer developmental trajectories and pseudotime from single-cell RNA-seq data using Monocle3, Slingshot, and scVelo for RNA velocity analysis.
☆ 300查看技能
GitHub
bio-methylation-dmr-detection
Differentially methylated region (DMR) detection using methylKit tiles, bsseq BSmooth, and DMRcate. Use when identifying contiguous genomic regions with methylation differences between experimental conditions o...
☆ 300查看技能
默认按已收录数据中的 GitHub 仓库 Stars 排序。Stars 属于来源仓库，同一仓库的多个技能可能共享相同数值；它反映仓库关注度，不代表单个技能的安装量或质量评分。