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Data & Analytics
Data analysis, BI, visualization, datasets, statistics, and ML workflows
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- Short Read AssemblyDe 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. Use when assembling genomes from Illumina reads.Votes: 0GitHub stars: 171
- Sequence PropertiesCalculate sequence properties like GC content, molecular weight, isoelectric point, and GC skew using Biopython. Use when analyzing sequence composition, computing physical properties, or comparing sequences.Votes: 0GitHub stars: 171
- Seq ObjectsCreate 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.Votes: 0GitHub stars: 171
- Selection StatisticsDetect signatures of natural selection using Fst, Tajima's D, iHS, XP-EHH, and other selection statistics. Calculate population differentiation, test for departures from neutrality, and identify selective sweeps with scikit-allel and vcftools. Use when computing selection signatures like Fst or Tajima's D.Votes: 0GitHub stars: 171
- Secondary Structure PredictionPredicts RNA secondary structures using minimum free energy folding and partition function analysis with ViennaRNA (RNAfold, RNAalifold, RNAcofold). Computes base-pair probabilities, centroid structures, and consensus structures from alignments. Use when predicting RNA folding, evaluating structural stability, or comparing structures across homologs.Votes: 0GitHub stars: 171
- Scrnaseq PipelineEnd-to-end single-cell RNA-seq workflow from 10X Genomics data to annotated cell types. Covers QC, normalization, clustering, marker detection, and cell type annotation. Use when analyzing single-cell RNA-seq data.Votes: 0GitHub stars: 171
- Screen QcQuality control for pooled CRISPR screens covering library representation, Gini index, log-skew, replicate Pearson and Spearman concordance, essentialome precision-recall AUC against CEGv2 (Hart 2017), Cas9 cut-toxicity diagnostics, copy-number amplicon detection (Aguirre 2016 / Munoz 2016), bottleneck propagation through plasmid pool, infection, selection, and endpoint stages, MOI verification, and DepMap-style screen-quality scoring. Use when assessing screen quality before hit calling, dec...Votes: 0GitHub stars: 171
- Scikit Allel AnalysisPython population genetics with scikit-allel. Read VCF files, compute allele frequencies, calculate diversity statistics, perform PCA, and run selection scans using GenotypeArray and HaplotypeArray data structures. Use when analyzing population genetics in Python.Votes: 0GitHub stars: 171
- Scenic RegulonsInfer gene regulatory networks and identify transcription factor regulons from single-cell RNA-seq data using pySCENIC. Discovers co-expression modules with GRNBoost2, prunes by cis-regulatory motif enrichment, and scores regulon activity per cell with AUCell. Use when identifying transcription factor regulons, scoring TF activity in single cells, or finding master regulators of cell identity.Votes: 0GitHub stars: 171
- ScaffoldingScaffold contigs into chromosome-level assemblies using Hi-C data with YaHS, 3D-DNA, SALSA2, and validate with BUSCO and contact maps. Use when scaffolding contigs to chromosome-level assemblies.Votes: 0GitHub stars: 171
- Scaffold AnalysisAnalyzes chemical libraries by scaffold using Bemis-Murcko scaffolds, generic frameworks, cyclic skeletons, matched molecular pair (MMP) analysis via mmpdb, R-group decomposition, Free-Wilson analysis, scaffold hopping, and chemotype-aware ML train/test splits. Use when identifying chemotype clusters in a library, deriving SAR transformation rules, decomposing series into R-groups, performing scaffold-balanced QSAR splits, or planning analog campaigns.Votes: 0GitHub stars: 171
- JupyterAssists with interactive data analysis, visualization, and reproducible research using Jupyter notebooks. Use when building notebooks that combine code with rich output, managing kernels, converting to reports, or parameterizing notebooks for batch execution. Trigger words: jupyter, notebook, jupyterlab, ipynb, nbconvert, papermill.Votes: 0GitHub stars: 142
- Sashimi PlotsCreates sashimi-style plots showing RNA-seq read coverage and splice junction counts using ggsashimi (general-purpose, condition-grouped overlays), rmats2sashimiplot (rMATS-output-aware), MAJIQ-VOILA (LSV posteriors interactive HTML), leafviz (leafcutter clusters Shiny), Jutils (tool-agnostic heatmaps and sashimi for rMATS/leafcutter/SUPPA2/MAJIQ output), or pyGenomeTracks (multi-track publication figures). Tool choice depends on the upstream differential-splicing tool's output format and the...Votes: 0GitHub stars: 171
- Sample SizeEstimates required sample sizes for differential expression, ChIP-seq, methylation, and proteomics studies. Use when budgeting experiments, writing grant proposals, or determining minimum replicates needed to achieve statistical significance for expected effect sizes.Votes: 0GitHub stars: 171
- Sam Bam BasicsView, convert, and understand SAM/BAM/CRAM alignment files using samtools and pysam. Use when inspecting alignments, converting between formats, or understanding alignment file structure.Votes: 0GitHub stars: 171
- Rnaseq To DeEnd-to-end RNA-seq workflow from FASTQ files to differential expression results. Covers QC, quantification (Salmon or STAR+featureCounts), and DESeq2 analysis with visualization. Use when running RNA-seq from FASTQ to DE results.Votes: 0GitHub stars: 171
- Rmarkdown ReportsCreate reproducible bioinformatics analysis reports with R Markdown including code, results, and visualizations in HTML, PDF, or Word format. Use when generating analysis reports with RMarkdown.Votes: 0GitHub stars: 171
- Riboseq PipelineEnd-to-end Ribo-seq analysis from FASTQ to translation efficiency and ORF detection. Use when analyzing ribosome profiling data to study translation.Votes: 0GitHub stars: 171
- Restriction MappingCreate restriction maps showing enzyme cut positions on DNA sequences using Biopython Bio.Restriction. Visualize cut sites, calculate distances between sites, and generate text or graphical maps. Use when creating or analyzing restriction maps.Votes: 0GitHub stars: 171
- Repeat AnnotationIdentify and classify repetitive elements and transposable elements using RepeatModeler for de novo repeat library construction and RepeatMasker for genome-wide repeat annotation. Quantify TE expression from RNA-seq with TEtranscripts. Use when masking repeats before gene prediction or analyzing transposable element activity.Votes: 0GitHub stars: 171
- Remote HomologyDetect distant homologs using profile and structure-aware methods that go beyond standard BLAST. Use when sequence identity falls into the twilight zone (<35% pairwise), when BLAST fails to find homologs that should exist, when working at metagenomic scale (DIAMOND, MMseqs2), or when structure beats sequence (Foldseek). Covers PSI-BLAST (iterative PSSM), jackhmmer (iterative HMM), HHblits/HHsearch (profile-profile), DIAMOND, MMseqs2, and Foldseek (3Di structural alphabet, van Kempen 2024).Votes: 0GitHub stars: 171
- Reference PanelsDownload, 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 for target populations.Votes: 0GitHub stars: 171
- Recurrent CnvIdentify recurrent and driver copy number alterations across a tumor cohort with GISTIC2 (G-score, Ziggurat deconstruction, focal vs broad/arm-level analysis, q-values from permutation) and quantify copy-number signatures with the Steele 2022 COSMIC framework and the Drews 2022 CINSignatures framework. Covers driver-gene localization from recurrence peaks, distinguishing focal drivers from arm-level passengers, and the caller-sensitivity caveats of copy-number signatures. Use when finding rec...Votes: 0GitHub stars: 171
- Reactome PathwaysReactome pathway enrichment using ReactomePA package. Use when analyzing gene lists against Reactome's curated peer-reviewed pathway database. Performs over-representation analysis and GSEA with visualization and pathway hierarchy exploration.Votes: 0GitHub stars: 171