69 projects
pymclustR
Pure-Python re-implementation of CRAN mclust — Gaussian mixture model clustering with all 14 covariance parameterizations, AnnData-native.
pyurd-bio
Pure-Python port of URD — branching pseudotime / tree inference (Farrell et al. Science 2018).
pyslingshot-bio
Pure-Python port of slingshot — cell-lineage and pseudotime inference (Street et al. BMC Genomics 2018).
pymonocle3-bio
omicverse-facing wrapper for Bio-Babel/Monocle3-python — Python port of R monocle3.
pydynwrap-bio
Pure-Python port of dynwrap — single-cell trajectory data wrapper (Saelens et al. Nat Biotechnol 2019).
pydyneval-bio
Pure-Python port of dyneval — trajectory inference benchmark metrics (Saelens et al. Nat Biotechnol 2019).
pydynbenchmark
Trajectory inference benchmarking — Python implementation of dyneval-family metrics + synthetic generators (Saelens et al. Nat Biotechnol 2019).
pydestiny-bio
Pure-Python port of destiny — diffusion maps + DPT for single-cell RNA-seq (Angerer et al. 2016).
pycytotrace-bio
Pure-Python port of CytoTRACE — gene-count-based stemness pseudotime (Gulati et al. Science 2020).
pyfunkyheatmap
Pure-Python port of the R funkyheatmap package — generate publication-ready dataframe heatmaps with funky rectangles, pies, bars and more.
mudataoom
Out-of-memory MuData — drop-in replacement for mudata.MuData built on mudata-rs and anndataoom
pycondiments
Pure-Python port of condiments — differential trajectory analysis across conditions (Roux de Bezieux et al. Nat Commun 2024).
pytradeseq
Pure-Python port of tradeSeq — trajectory-based differential expression analysis for scRNA-seq (Van den Berge et al. 2020).
pyscorpius
Pure-Python port of SCORPIUS — linear-trajectory inference for single-cell RNA-seq via MDS + principal curves.
fpocket-rs
Rust reimplementation of the fpocket protein binding-pocket detection algorithm — pip-installable, no qhull/conda required.
pysccdc
Pure-Python port of the R package scCDC — entropy-based, gene-specific ambient-RNA contamination detection and correction for scRNA-seq / snRNA-seq.
pydecontx
Pure-Python port of the Bioconductor decontX package — decontamination of ambient RNA in single-cell RNA-seq via a Bayesian two-component multinomial mixture.
pysoupx
Pure-Python port of the R package SoupX — removal of ambient (soup) RNA contamination from droplet-based single-cell RNA-seq data.
pyfastcar
Pure-Python port of the R package FastCAR — fast, deterministic per-gene ambient-RNA correction for droplet-based single-cell RNA-seq.
pygliph
Pure-Python port of the R package turboGliph — GLIPH and GLIPH2 specificity-group clustering of T-cell receptor CDR3 repertoires.
pytigger
Pure-Python port of the R/CRAN package tigger — novel immunoglobulin V-allele discovery and subject-specific V genotype inference from AIRR-Seq / Rep-Seq data.
pydowser
Pure-Python port of the R/CRAN package dowser - B-cell receptor phylogenetics: lineage trees, measurable evolution, migration/differentiation tests (Immcantation).
pyimmunarch
Pure-Python port of the R package immunarch — bulk and single-cell immune-repertoire (TCR/BCR AIRR-seq) analytics.
pyalakazam
Pure-Python port of the R/CRAN package alakazam -- the core package of the Immcantation framework for adaptive immune receptor repertoire (AIRR-seq) analysis.
pyscoper
Pure-Python port of the R/CRAN package scoper — spectral, hierarchical and identity clustering for B-cell clonal partitioning (Immcantation).
pyshazam
Pure-Python port of the R/CRAN package shazam -- immunoglobulin somatic hypermutation (SHM) analysis: distance-to-nearest, clonal threshold, SHM targeting models, mutation profiling and BASELINe selection analysis.
pymfuzz
Pure-Python port of Bioconductor Mfuzz — soft clustering of time-series gene-expression data by fuzzy c-means.
pytwas
Pure-Python reimplementation of TWAS (MetaXcan / S-PrediXcan / S-MultiXcan / PrediXcan) — transcriptome-wide association study.
pytwosamplemr
Pure-Python port of two-sample Mendelian randomization — the MendelianRandomization estimator suite plus the TwoSampleMR harmonisation / diagnostics workflow.
pyldsc
Modern-Python reimplementation of LDSC (LD Score Regression) -- SNP-heritability, genetic correlation, partitioned/stratified h2 and LDSC-SEG cell-type enrichment.
pyscdrs
Clean pure-Python reimplementation of scDRS — single-cell disease-relevance scoring from GWAS gene sets.
pycoloc
Pure-Python port of the R package coloc — Bayesian colocalisation of two genetic traits via Approximate Bayes Factors and SuSiE.
pysusie
Pure-Python port of the R/CRAN package susieR — Sum of Single Effects (SuSiE) regression for Bayesian variable selection and genetic fine-mapping.
pymatrixeqtl
Pure-Python port of CRAN MatrixEQTL -- ultra-fast eQTL mapping (linear / ANOVA / interaction models, cis/trans split, Benjamini-Hochberg FDR).
pylipidr
Pure-Python port of Bioconductor lipidr — lipidomics data analysis, normalization, differential analysis and lipid-set enrichment (LSEA).
python-limma
Pure-Python port of Bioconductor limma — linear models & empirical-Bayes moderated statistics for differential expression (voom, lmFit, eBayes, topTable).
pyedger
Pure-Python port of Bioconductor edgeR — negative-binomial models for differential expression of count data (estimateDisp, glmFit, glmLRT, glmQLFTest, exactTest).
pymsstats
Pure-Python port of Bioconductor MSstats — vendor converters, pre-processing, normalization, summarization, group comparison, sample-size design, and QC plotting for mass-spec proteomics.
pyolinkanalyze
Pure-Python port of Olink Proteomics' R OlinkAnalyze — NPX I/O, bridge normalization, and per-protein differential expression for Olink proteomics.
pyproda
Pure-Python port of Bioconductor proDA — probabilistic dropout model for mass-spec proteomics differential abundance testing.
pydeqms
Pure-Python port of Bioconductor DEqMS — peptide-count-aware moderated t-tests for differential mass-spec proteomics.
pyimputelcmd
Pure-Python port of Bioconductor imputeLCMD — left-censored MNAR + MAR (MLE/KNN/SVD) imputation, model selection, and synthetic data for label-free proteomics.
omicverse
OmicVerse: A single pipeline for exploring the entire transcriptome universe
anndataoom
Out-of-memory AnnData powered by Rust (anndata-rs)
omicverse-skills
Standalone OmicVerse skills catalog
nmf-rs
Rust port of R NMF package — bit-equivalent multiplicative updates (brunet/lee/offset/nsNMF), parallelised with rayon.
bandnorm-rs
Rust port of BandNorm's scGAD + bandnorm normalization for single-cell Hi-C — bit-equivalent to the R reference, ~10-30× faster.
schicluster-rs
Rust port of scHiCluster's impute_chromosome inner pipeline — drop-in replacement for the published Python implementation. Bit-equivalent numerical behaviour, up to ~10× faster on long Hi-C chromosomes.
pyccasc
Pure-Python re-implementation of Seurat's CCA — canonical correlation analysis for single-cell integration, AnnData-native.
pyrun-cca
Pure-Python re-implementation of Seurat's CCA — canonical correlation analysis for single-cell integration, AnnData-native.
run-cca-py
Pure-Python re-implementation of Seurat's CCA — canonical correlation analysis for single-cell integration, AnnData-native.
pyseurat-cca
Pure-Python re-implementation of Seurat's CCA — canonical correlation analysis for single-cell integration, AnnData-native.
seurat-cca
Pure-Python re-implementation of Seurat's CCA — canonical correlation analysis for single-cell integration, AnnData-native.
seurat-cca-py
Pure-Python re-implementation of Seurat's CCA — canonical correlation analysis for single-cell integration, AnnData-native.
pydada2
Pure-Python DADA2 — exact amplicon sequence variant inference from amplicon sequencing data.
pyscdblfinder
Pure-Python scDblFinder — fast doublet detection in scRNA-seq via artificial-doublet xgboost classification, AnnData-native.
pydoubletfinder
Pure-Python DoubletFinder — computational doublet detection in scRNA-seq via artificial-doublet pANN scoring, AnnData-native.
omicverse-notebook
OmicVerse-inspired DataFrame and AnnData previews for JupyterLab
omicclaw
OmicClaw gateway-first workspace for web UI, channels, notebooks, and agent workflows
omicverseweb
OmicVerse web interface for single-cell analysis
epione
EpiOne: Generative cartography of single-cell epigenomes
pantheon-notebook
A JupyterLab extension for Pantheon CLI integration with floating input widget
pantheon-cli
Command Line Interface for Pantheon - A framework for building distributed evolvable multi-agent systems.
omicfate
OmicFate: Unraveling the Secrets of Cellular Fate Determination
scltnn
A library to calculate the latent time of scRNA-seq
Pyomic
A python framework library for omics analysis
ERgene
A python module that could analysis the ERGs
exDEG
A python library for screening classified dignosed Gene
ClassifyGene
A python library for screening classified dignosed Gene
