1,400 skills found · Page 37 of 47
jaechang-hits / muon-multiomics-singlecellMulti-modal single-cell analysis with muon/MuData. Joint RNA+ATAC (10x Multiome), CITE-seq (RNA+protein), other multi-omics. MuData holds per-modality AnnData with shared obs. WNN joint embedding, per-modality preprocessing, MOFA factor analysis.
jaechang-hits / reactome-databaseQuery Reactome pathways via REST: pathway queries, entity lookup, keyword search, gene list enrichment, hierarchy, cross-refs. Content + Analysis services. Python wrapper: reactome2py. For KEGG use kegg-database; for PPIs use string-database-ppi.
jaechang-hits / pysam-genomic-filesRead/write SAM/BAM/CRAM, VCF/BCF, FASTA/FASTQ. Region queries, pileup, variant filtering, read groups. Python htslib wrapper exposing samtools/bcftools CLI. Use STAR/BWA for alignment; GATK/DeepVariant for variant calling.
jaechang-hits / samtools-bam-processingCLI toolkit for SAM/BAM/CRAM: sort, index, convert, filter, QC alignments. Core commands: view, sort, index, flagstat, stats, depth, markdup, merge. Required between alignment and variant/peak calling. Use pysam for Python-native BAM access; deeptools for normalized coverage tracks.
jaechang-hits / bioservices-multi-databaseUnified Python interface to 40+ bioinformatics web services: UniProt proteins, KEGG pathways, ChEMBL/ChEBI/PubChem, BLAST, cross-database ID mapping, GO annotations, PPI.
jaechang-hits / ena-databaseENA REST API for sequences, reads, assemblies, and annotations. Portal API search, Browser API retrieval (XML/FASTA/EMBL), file reports for FASTQ/BAM URLs, taxonomy, cross-refs. For multi-DB Python use bioservices; for NCBI-only use pubmed-database or Biopython Entrez.
jaechang-hits / gget-genomic-databasesUnified CLI/Python interface to 20+ genomic databases. Gene lookups (Ensembl search/info/seq), BLAST/BLAT, AlphaFold, Enrichr enrichment, OpenTargets disease/drug, CELLxGENE single-cell, cBioPortal/COSMIC cancer, ARCHS4 expression. Spans genomics, proteomics, disease.
jaechang-hits / kegg-databaseKEGG REST API (academic only). Pathways, genes, compounds, enzymes, diseases, drugs via 7 ops (info/list/find/get/conv/link/ddi). ID conversion (NCBI/UniProt/PubChem). Use bioservices for multi-DB Python.
jaechang-hits / genimlPython library for genomic interval ML. Train/apply region2vec embeddings turning BED regions into vectors, index interval datasets for ML, search embedding space with BEDSpace, and evaluate embedding quality.
jaechang-hits / gtarsRust-backed Python library for fast genomic token arithmetic and BED processing. High-performance BED I/O, interval set ops (intersect, merge, complement, subtract), region tokenization against a universe, universe construction. Use for preprocessing large BED collections and ML token vocabularies.
jaechang-hits / deseq2-differential-expressionBulk RNA-seq DE with R/Bioconductor DESeq2. Negative binomial GLM, empirical Bayes shrinkage, Wald/LRT tests, multi-factor designs, Salmon tximeta import, apeglm LFC shrinkage, MA/volcano/heatmap viz. R gold standard. Use pydeseq2-differential-expression for Python; use edgeR for TMM normalization.
jaechang-hits / gseapy-gene-enrichmentGSEA and over-representation analysis (ORA) for RNA-seq and proteomics. Wraps Enrichr for ORA against MSigDB, KEGG, GO, and 200+ databases; runs preranked GSEA on ranked DE gene lists. Outputs enrichment tables and running-score plots. Use after DESeq2 or edgeR for pathway-level interpretation.
jaechang-hits / pydeseq2-differential-expressionBulk RNA-seq DE with PyDESeq2: load counts, normalize, fit negative binomial models, Wald test (BH-FDR), LFC shrinkage, volcano/MA plots. Use for two-group comparisons, multi-factor designs with batch correction, multiple contrasts.
jaechang-hits / harmony-batch-correctionHarmony batch correction for scRNA-seq and other omics. Removes batch effects from PCA embeddings while preserving biology. Run after PCA, before UMAP. Scales to millions of cells. Python (harmonypy, scanpy) and R (Seurat).
jaechang-hits / pathmlComputational pathology toolkit for whole-slide images (WSIs): load slides, extract tiles, stain normalization, nuclear segmentation, feature extraction, and ML training. Supports H&E and multiplex. For end-to-end pipelines from raw WSIs to quantitative outputs.
jaechang-hits / cancer-research-figure-guideCancer Research (AACR) figures: resolution (300-1200 DPI), formats (EPS/TIFF/AI), hierarchical panel labels (Ai, Aii, Bi), figure/table limits, legend requirements with replicate counts.
jaechang-hits / lancet-figure-guideThe Lancet figure preparation: resolution (300+ DPI at 120%), preferred editable formats (PowerPoint/Word/SVG), column widths (75/154 mm), Times New Roman, in-house redraw policy.
giuseppe-trisciuoglio / aws-lambda-python-integrationProvides AWS Lambda integration patterns for Python with cold start optimization
datadrivenconstruction / as-built-documentationAutomate as-built documentation and digital handover for construction. Compile project records, generate O&M manuals, create asset databases, and ensure complete project closeout.
datadrivenconstruction / bim-visual-programming-automationAutomate BIM workflows using visual programming and Python. Create parametric schedules, export data, batch modify elements, and integrate with external data sources.
datadrivenconstruction / capacity-planningPlan organizational capacity for construction projects. Forecast resource needs, identify capacity gaps, and support strategic planning for project pursuit and staffing.
datadrivenconstruction / change-order-analysisAnalyze and predict construction change orders using ML. Classify change order types, predict costs and schedule impacts, identify patterns, and optimize approval workflows.
datadrivenconstruction / clash-detection-analysisDetect and analyze geometric clashes between BIM elements. Identify hard clashes, soft clashes, and workflow conflicts using spatial analysis and rule-based detection.
datadrivenconstruction / contractor-matching-aiAI-powered contractor matching and selection for construction projects. Analyze contractor capabilities, past performance, certifications, and project requirements to recommend optimal matches.
datadrivenconstruction / defect-detection-aiAI-powered construction defect detection using computer vision. Identify cracks, spalling, corrosion, and other defects in concrete, steel, and building components from images and video.
datadrivenconstruction / digital-twin-syncSynchronize construction digital twins with real-time data. Connect BIM models with IoT sensors, progress updates, and field data for live project visualization and monitoring.
datadrivenconstruction / document-classification-nlpAutomatically classify and extract information from construction documents using NLP. Categorize RFIs, submittals, change orders, specifications, and contracts.
datadrivenconstruction / drone-site-surveyProcess drone survey data for construction sites. Generate orthomosaics, DEMs, point clouds, calculate volumes, track progress, and integrate with BIM models for comparison.
datadrivenconstruction / energy-simulationBuilding energy simulation and analysis for construction. Calculate heating/cooling loads, evaluate envelope performance, optimize HVAC sizing, and ensure energy code compliance.
datadrivenconstruction / enterprise-risk-aggregatorAggregate and analyze risks across construction project portfolio. Identify correlated risks, systemic exposures, and portfolio-level risk mitigation strategies.
