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.
☆ 300查看技能
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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...
☆ 300查看技能
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.
☆ 300查看技能
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.
☆ 300查看技能
GitHub
bio-crispr-library-design
CRISPR library design for genetic screens. Covers sgRNA selection, library composition, control design, and oligo ordering. Use when designing custom sgRNA libraries for knockout, activation, or interference sc...
☆ 300查看技能
GitHub
bio-workflows-multiome-pipeline
End-to-end multiome workflow for joint scRNA-seq + scATAC-seq analysis. Covers data loading, separate modality processing, and WNN integration with Seurat/Signac.
☆ 300查看技能
GitHub
bio-proteomics-quantification
Protein quantification from mass spectrometry data including label-free (LFQ, intensity-based), isobaric labeling (TMT, iTRAQ), and metabolic labeling (SILAC) approaches. Use when extracting protein abundances...
☆ 300查看技能
GitHub
bio-flow-cytometry-bead-normalization
Bead-based normalization for CyTOF and high-parameter flow cytometry. Covers EQ bead normalization, signal drift correction, and batch normalization. Use when correcting instrument drift in CyTOF or harmonizing...
☆ 300查看技能
GitHub
bio-genome-assembly-assembly-qc
Assess genome assembly quality using QUAST for contiguity metrics and BUSCO for completeness. Essential for evaluating assembly success and comparing assemblers.
☆ 300查看技能
GitHub
bio-spatial-transcriptomics-image-analysis
Process and analyze tissue images from spatial transcriptomics data using Squidpy. Extract image features, segment cells/nuclei, and compute morphological features from H&E or IF images.
☆ 300查看技能
GitHub
bio-filter-sequences
Filter and select sequences by criteria (length, ID, GC content, patterns) using Biopython. Use when subsetting sequences, removing unwanted records, or selecting by specific criteria.
☆ 300查看技能
GitHub
bio-genome-assembly-short-read-assembly
De novo genome assembly from Illumina short reads using SPAdes. Covers bacterial, fungal, and small eukaryotic genome assembly, as well as metagenome and transcriptome assembly modes.
☆ 300查看技能
GitHub
bio-restriction-enzyme-selection
Select restriction enzymes by criteria using Biopython Bio.Restriction. Find enzymes that cut once, don't cut, produce specific overhangs, are commercially available, or have compatible ends for cloning.
☆ 300查看技能
GitHub
bio-metabolomics-normalization-qc
Quality control and normalization for metabolomics data. Covers QC-based correction, batch effect removal, and data transformation methods. Use when correcting technical variation in metabolomics data before st...
☆ 300查看技能
GitHub
bio-imaging-mass-cytometry-phenotyping
Cell type assignment from marker expression in IMC data. Covers manual gating, clustering, and automated classification approaches. Use when assigning cell types to segmented IMC cells based on protein marker e...
☆ 300查看技能
GitHub
bio-population-genetics-plink-basics
PLINK file formats, format conversion, and quality control filtering for population genetics. Convert between VCF, BED/BIM/FAM, and PED/MAP formats, apply MAF, genotyping rate, and HWE filters using PLINK 1.9 a...
☆ 300查看技能
GitHub
bio-hi-c-analysis-matrix-operations
Balance, normalize, and transform Hi-C contact matrices using cooler and cooltools. Apply iterative correction (ICE), compute expected values, and generate observed/expected matrices.
☆ 300查看技能
GitHub
bio-seq-objects
Create and manipulate Seq, MutableSeq, and SeqRecord objects using Biopython. Use when creating sequences from strings, modifying sequence data in-place, or building annotated sequence records.
☆ 300查看技能
GitHub
to-spring-or-not-to-spring
Decision framework for choosing between easing curves and springs in interface motion. Use when implementing animations, reviewing motion feel, or debugging why an animation feels wrong. Triggers on tasks invol...
☆ 300查看技能
GitHub
artifacts-builder
Automates the release process for the ts-oauth2-server project.
☆ 299查看技能
GitHub
bio-reporting-rmarkdown-reports
Create reproducible bioinformatics analysis reports with R Markdown including code, results, and visualizations in HTML, PDF, or Word format.
☆ 299查看技能
GitHub
bio-reporting-quarto-reports
Build reproducible scientific documents, presentations, and websites with Quarto supporting R, Python, Julia, and Observable JS.
☆ 299查看技能
GitHub
bio-data-visualization-color-palettes
Select and apply colorblind-friendly palettes for scientific figures using viridis, RColorBrewer, and custom color schemes.
☆ 299查看技能
GitHub
bio-entrez-link
Find cross-references between NCBI databases using Biopython Bio.Entrez. Use for navigating from genes to proteins, sequences to publications, finding related records, and discovering database relationships.
☆ 299查看技能
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