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Data & Analytics
Data analysis, BI, visualization, datasets, statistics, and ML workflows
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- Super EnhancersIdentifies super-enhancers from H3K27ac, MED1, or BRD4 ChIP-seq using ROSE, ROSE2, LILY, HOMER -style super, and ENCODE dELS cross-referencing. Handles peak stitching parameters, ranking choices, hockey-stick inflection, marker choice (H3K27ac vs MED1/BRD4), and cross-condition comparison with spike-in normalization. Constructs core regulatory circuitry (Saint-Andre 2016) from SE-encoded TFs. Use when identifying cell-identity / cancer-associated regulatory domains, comparing super-enhancers ...Votes: 0GitHub stars: 171
- MalloyMalloy is an open-source semantic modeling and query language that compiles to SQL and runs on DuckDB, BigQuery, Snowflake, PostgreSQL, MySQL, Trino, Presto and Databricks. Use when the user wants to write Malloy models, sources, views, joins or nested queries, run .malloy files from the VS Code extension, the malloy-cli command line or Node.js, or replace repetitive SQL analytics with reusable measures.Votes: 0GitHub stars: 142
- Subgroup AnalysisPerforms subgroup and heterogeneous treatment effect (HTE) analyses for clinical trials. Covers Mantel-Haenszel pooling, Breslow-Day, interaction tests in regression, RERI for additive interaction, modern data-adaptive HTE methods (STEPP, SIDES, causal forests, X/R-learners), Bayesian shrinkage (Dixon-Simon, MAP, EXNEX), graphical multiplicity (Bretz-Maurer), and credibility frameworks (Sun BMJ, EMA 2019). Use when analyzing treatment effects across patient subgroups for regulatory submission...Votes: 0GitHub stars: 171
- Subclonal Copy NumberResolve subclonal copy number, whole-genome doubling, and copy-number tumor evolution from bulk sequencing with Battenberg, TITAN, and MEDICC2. Covers clonal versus subclonal copy-number states, haplotype phasing for subclonal resolution, cancer cell fraction, whole-genome-doubling detection and timing relative to mutations, mirrored subclonal allelic imbalance, and copy-number phylogenies. Use when a tumor is heterogeneous and bulk data shows non-integer copy number, when calling subclonal C...Votes: 0GitHub stars: 171
- Structure ProbingAnalyzes experimental RNA structure probing data from SHAPE-MaP and DMS-MaPseq experiments using ShapeMapper2. Converts mutation rates to per-nucleotide reactivity profiles that constrain structure prediction. Use when processing SHAPE-MaP or DMS-MaPseq sequencing data to obtain experimental RNA structure information.Votes: 0GitHub stars: 171
- Structural Variant CallingCall structural variants (SVs) from sequencing data using Manta, Delly, GRIDSS, and LUMPY. Detects deletions, insertions, inversions, duplications, and translocations too large for standard SNV callers. Use when detecting structural variants from short-read or long-read data and building consensus callsets.Votes: 0GitHub stars: 171
- Structural AlignmentAlign protein structures using Foldseek 3Di, TM-align, US-align, DALI, or Foldmason for structural MSA. Predict, score, and superpose backbone coordinates when sequence identity is below the twilight zone or remote-homology detection is required. Use when sequence MSA fails (<25% identity), when the dark proteome is the target, when AlphaFoldDB / ESM Atlas search is needed, or when structural superposition is the goal.Votes: 0GitHub stars: 171
- Statistical AnalysisStatistical analysis for metabolomics data. Covers preprocessing (log2 transformation, normalization), limma moderated testing with empirical Bayes, Welch's t-tests with BH correction, fold change estimation, and multivariate methods (PCA, PLS-DA, OPLS-DA). Use when identifying differentially abundant metabolites or building classification models.Votes: 0GitHub stars: 171
- Star AlignmentAlign RNA-seq reads with STAR (Spliced Transcripts Alignment to a Reference). Supports two-pass mode for novel splice junction discovery. Use when aligning RNA-seq data requiring splice-aware alignment.Votes: 0GitHub stars: 171
- Sra DataDownload raw sequencing reads from NCBI SRA using sra-tools (prefetch, fasterq-dump, vdb-validate) or the ENA mirror. Use when pulling FASTQ for SRR/ERR/DRR accessions, deciding between SRA-direct, ENA mirror, or AWS/GCP cloud mirror (STRIDES), handling --include-technical for 10x and other single-cell records, validating with MD5/vdb-validate, navigating SRR/SRX/SRS/SRP/PRJNA hierarchy, or finding accessions via pysradb. Encodes SRA cloud-egress economics, the fasterq-dump uncompressed-scrat...Votes: 0GitHub stars: 171
- Splicing QuantificationQuantifies alternative splicing as PSI (percent spliced in) from RNA-seq using rMATS-turbo (BAM-based event), SUPPA2 (TPM-based event), MAJIQ V3 (LSV-based Bayesian), leafcutter (annotation-free intron clusters), VAST-TOOLS (cross-species with microexon support), Shiba (junction-imbalance-corrected, 2025 SOTA at low coverage), or IRFinder-S (intron retention coverage-aware). Distinguishes the five canonical event classes (SE, A5SS, A3SS, MXE, RI), special classes (microexons, exitrons, AFE/AL...Votes: 0GitHub stars: 171
- Splicing QcAssesses RNA-seq data quality specifically for alternative splicing analysis. QC layers include experimental design audit (library prep, read length, depth, replicates), STAR 2-pass cohort-style alignment, junction saturation curves and discovery plateau detection, novel-vs-known junction ratio diagnostics, junction-overhang distribution, splice-site strength scoring (MaxEntScan intrinsic + SpliceAI context-aware), strandedness verification, GENCODE basic vs comprehensive choice, and rRNA con...Votes: 0GitHub stars: 171
- Splicing PipelineEnd-to-end alternative splicing analysis from FASTQ to differential splicing results for short-read bulk RNA-seq. Aligns with STAR 2-pass cohort-style, performs junction QC (RSeQC, MaxEntScan, SpliceAI), runs rMATS-turbo and leafcutter for concordant differential analysis, optionally MAJIQ V3 for complex events / heterogeneous cohorts, isoform-switching with NMD/ORF/domain consequences (IsoformSwitchAnalyzeR v2 + DRIMSeq+DEXSeq+stageR DTU), and sashimi visualizations. Use when performing comp...Votes: 0GitHub stars: 171
- Spike In NormalizationNormalizes ChIP-seq data using exogenous spike-in (ChIP-Rx with Drosophila chromatin per Orlando 2014 / Egan 2016; E. coli carryover for CUT&RUN/CUT&Tag). Distinguishes RRPM from Rx-Input scaling, integrates with DiffBind / DESeq2 / edgeR / csaw via sizeFactors and DiffBind library-size vectors, and applies the Patel et al 2024 *Nat Biotechnol* review's failure-mode framework to validate that normalization is correctly applied at the read level (not peak counts). Use when global signal shifts...Votes: 0GitHub stars: 171
- Species TreesEstimate species trees using coalescent methods including ASTRAL-III, wASTRAL, ASTRAL-Pro, SVDQuartets, and BPP. Use when multi-locus data shows gene tree discordance from incomplete lineage sorting, when in the anomaly zone where concatenation is misleading, or when computing concordance factors to assess topological support.Votes: 0GitHub stars: 171
- Species DelimitationDelimits species boundaries from molecular data using distance-based (ASAP), tree-based (bPTP, GMYC), and coalescent (BPP) methods. Compares multiple delimitation results with delimtools. Use when delineating putative species from DNA barcoding data, resolving cryptic species complexes, or validating taxonomic assignments. Emphasizes multi-method consensus following integrative taxonomy best practice.Votes: 0GitHub stars: 171
- Spatial PipelineEnd-to-end spatial transcriptomics workflow for Visium/Xenium data. Covers data loading, preprocessing, spatial analysis, domain detection, and visualization with Squidpy. Use when analyzing spatial transcriptomics data.Votes: 0GitHub stars: 171
- Sparse HandlingWork with sparse matrices for memory-efficient storage of count data. Use when dealing with single-cell data or large bulk RNA-seq datasets where most values are zero.Votes: 0GitHub stars: 171
- Somatic Variant PipelineEnd-to-end somatic variant calling from tumor-normal paired samples using Mutect2 or Strelka2. Covers preprocessing, variant calling, filtering, and annotation for cancer genomics. Use when calling somatic mutations from tumor-normal pairs.Votes: 0GitHub stars: 171
- Somatic SignaturesExtracts and assigns COSMIC v3.4 mutational signatures (84 SBS / 11 DBS / 18 ID / 24 CN / 16 SV) from somatic VCFs using SigProfilerSuite, MutationalPatterns, MuSiCal mvNMF, SigNet, or HRDetect. Use when characterizing DNA-damage etiology (BRCA1/2 HRD, MMR-D, POLE, APOBEC3A, UV, tobacco, aflatoxin, 5-FU/SBS17b, platinum, colibactin SBS88), routing PARP inhibitor decisions, or auditing de novo extraction vs refit choice for cohort size.Votes: 0GitHub stars: 171
- Snakemake WorkflowsBuild reproducible bioinformatics pipelines with Snakemake using rules, wildcards, and automatic dependency resolution. Use when creating Python-based workflows, automating multi-step analyses with make-like dependency tracking, or running pipelines on HPC clusters with SLURM.Votes: 0GitHub stars: 171
- Smrna PreprocessingPreprocess small RNA sequencing data with adapter trimming and size selection optimized for miRNA, piRNA, and other small RNAs. Use when preparing small RNA-seq reads for downstream quantification or discovery analysis.Votes: 0GitHub stars: 171
- Smrna PipelineEnd-to-end small RNA-seq analysis from FASTQ to differential miRNA expression. Use when analyzing miRNA, piRNA, or other small RNA sequencing data.Votes: 0GitHub stars: 171
- Single Cell SplicingAnalyzes alternative splicing at single-cell resolution. The first decision is library chemistry — 10X 3' is fundamentally limited (RT primes from poly-A, R2 falls in 3' UTR, <0.1 junction read per cell per AS event). Plate-based full-length methods (Smart-seq3, FLASH-seq, VASA-seq, STORM-seq) and single-cell long-read (MAS-Iso-seq, scISOr-Seq2) are the chemistries that give per-cell isoform structure. Tools include MARVEL (R, Smart-seq integrated), BRIE2 (Bayesian PSI with regulatory feature...Votes: 0GitHub stars: 171