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theislab

23 indexed repositories · View on GitHub

single-cell-best-practices
https://www.sc-best-practices.org

Jupyter Notebook · 1267 stars
scarches
Reference mapping for single-cell genomics

Jupyter Notebook · 410 stars
ehrapy
Electronic Health Record Analysis with Python.

Python · 361 stars
single-cell-transformer-papers

HTML · 343 stars
moscot
Multi-omic single-cell optimal transport tools

Python · 216 stars
CellFlow
Modeling complex perturbations with CellFlow

Python · 159 stars
anndata2ri
Convert between AnnData and SingleCellExperiment

Python · 153 stars
destiny
R package for single cell and other data analysis using diffusion maps

R · 113 stars
DRVI
Unsupervised Deep Disentangled Representation of Single-Cell Omics

Python · 82 stars
scConcept
Contrastive pre-training for technology-agnostic single-cell representations beyond reconstruction

Python · 38 stars
CellHermes
LoRA finetuned LLM for single cell genomics research

Python · 31 stars
embpy

Python · 22 stars
ReconEval
Benchmarking for gene expression from single cell latent representations

Jupyter Notebook · 21 stars
cellink
Scalable framework for integrating single-cell omics with genetic data using AnnData.

Python · 21 stars
geome

Python · 17 stars
ehrdata
A datastructure for EHR data

Python · 15 stars
interscale
InterScale: multi-scale cellular interaction analysis model for spatial transcriptomics

Python · 12 stars
scanpydoc
Collection of Sphinx extensions similar to (but more flexible than) numpydoc

Python · 12 stars
gh-dashboard
A dashboard of everything in the theislab GitHub repository

HTML · 8 stars
sckitflow

Python · 7 stars
3 more repositories live on View on GitHub

Beginner friendly Everything

Open All

sparse.COO support for harmonize_missing_values and infer_feature_types Open

Difficulty 4/5 3-5 days Newbie friendliness 48/100

theislab/ehrdata#305 · Opened Sep 18, 2026
write_h5ed cannot write the output of io.omop.setup_obs Open

theislab/ehrdata#303 · 1 assignee · Opened Sep 14, 2026
`ep.pl.timeseries` and `ep.pl.variable_correlations` don't support the default `.X` storage for 3D data Open

Difficulty 3/5 1-2 days Newbie friendliness 78/100

theislab/ehrapy#1119 · 1 reaction · Opened Sep 8, 2026
Add the imputation notebook to the notebook CI checks Open

theislab/ehrapy#1118 · 1 comment · 1 assignee · Opened Sep 8, 2026
`mcar_test(method="little")` diverges from pyampute's reference Open

Difficulty 3/5 1-2 days Newbie friendliness 78/100

theislab/ehrapy#1110 · 1 reaction · Opened Aug 31, 2026
Move to cloudflare pages Open

enhancement

Difficulty 4/5 3-5 days Newbie friendliness 35/100

theislab/single-cell-best-practices#480 · Opened Aug 29, 2026
GraphOTTOutput.transport_matrix returns the expanded (n+m)² matrix, not the (n, m) block Open

Difficulty 3/5 1-2 days Newbie friendliness 64/100

theislab/moscot#847 · Opened Aug 24, 2026
GSEA figure Open

enhancement

theislab/single-cell-best-practices#460 · 1 reaction · 1 assignee · Opened Aug 13, 2026
ehrapy.pl wrappers are incompatible with scanpy's scanpy-v2-preview preset (scanpy 1.13.0a1) Open

Difficulty 4/5 3-5 days Newbie friendliness 55/100

theislab/ehrapy#1102 · Opened Aug 13, 2026
Own the port comparison here: squidpy no longer replays the reference bundle Open

Difficulty 5/5 Over a week Newbie friendliness 38/100

theislab/squidpy-ports#1 · Opened Aug 11, 2026
Release an updated PDF version of the book Open

enhancement

theislab/single-cell-best-practices#458 · 3 comments · 1 assignee · Opened Aug 6, 2026
Remove unecessary abstractions in `data` module. Open

bug

Difficulty 3/5 1-2 days Newbie friendliness 38/100

theislab/sckitflow#155 · Opened Aug 4, 2026
Docstring doesn't match manuscript's method: metric_energy_distance Open

Difficulty 1/5 Under an hour Newbie friendliness 78/100

theislab/ReconEval#4 · 1 comment · Opened Aug 3, 2026
write_continuous_cond_cov_to_step_data fails when StepData carries a plain dict of conditions Open

Difficulty 3/5 1-2 days Newbie friendliness 58/100

theislab/sckitflow#146 · Opened Jul 31, 2026
ot_quadratic_coupling rejects the optional linear terms when they are None Open

Difficulty 2/5 1-3 hours Newbie friendliness 88/100

theislab/sckitflow#145 · Opened Jul 31, 2026
SetEncoder: covariate validation raises ValueError, leaves 'No condition covariate found' unreachable Open

Difficulty 3/5 1-2 days Newbie friendliness 58/100

theislab/sckitflow#144 · Opened Jul 31, 2026
SetEncoder: covariates excluded from pooling keep the set axis Open

Difficulty 3/5 1-2 days Newbie friendliness 72/100

theislab/sckitflow#143 · Opened Jul 31, 2026
callbacks have weak contracts Open

Difficulty 5/5 Over a week Newbie friendliness 35/100

theislab/sckitflow#142 · Opened Jul 31, 2026
make data containers typed dict Open

Difficulty 5/5 Over a week Newbie friendliness 25/100

theislab/sckitflow#136 · Opened Jul 30, 2026
decide where preprocessing should belong Open

Difficulty 5/5 Over a week Newbie friendliness 20/100

theislab/sckitflow#132 · Opened Jul 29, 2026
we don't need adata in compile_adata because only obs is enough Open

Difficulty 3/5 1-2 days Newbie friendliness 35/100

theislab/sckitflow#130 · Opened Jul 29, 2026
don't make preprocessing part of the training loop Open

Difficulty 4/5 3-5 days Newbie friendliness 28/100

theislab/sckitflow#126 · Opened Jul 29, 2026
feature: cross dataset training interface changes Open

enhancement

Difficulty 5/5 Over a week Newbie friendliness 25/100

theislab/sckitflow#124 · Opened Jul 28, 2026
PolyForm license in pyproject.toml Open

bug

Difficulty 1/5 Under an hour Newbie friendliness 68/100

theislab/CellFlow#311 · Opened Jul 27, 2026
being able to load in memory per path Open

Difficulty 3/5 1-2 days Newbie friendliness 48/100

theislab/scfit#2 · Opened Jul 26, 2026
no random default state for PCA Open

Difficulty 2/5 1-3 hours Newbie friendliness 48/100

theislab/scConcept_rep#7 · 1 comment · Opened Jul 21, 2026
Numpy and Pandas Conflict Open

Difficulty 3/5 1-2 days Newbie friendliness 42/100

theislab/scarches#284 · Opened Jul 16, 2026
Documentation update: replace .layers["tem_data"] with `.X` Open

theislab/ehrapy#1093 · 1 reaction · 1 assignee · Opened Jul 14, 2026
Data Integration Needs Cancer Section Open

enhancement

Difficulty 4/5 3-5 days Newbie friendliness 35/100

theislab/single-cell-best-practices#450 · 1 comment · 1 reaction · Opened Jun 29, 2026
Pip install error Open

bug

Difficulty 3/5 1-2 days Newbie friendliness 45/100

theislab/embpy#38 · 1 comment · Opened Jun 23, 2026
Add scIB Open

enhancement

Difficulty 4/5 3-5 days Newbie friendliness 35/100

theislab/embpy#37 · Opened Jun 23, 2026
Release Open

theislab/cellink#124 · 4 comments · 1 assignee · Opened Jun 22, 2026
Fix docs build Open

bug

Difficulty 4/5 3-5 days Newbie friendliness 45/100

theislab/embpy#36 · Opened Jun 17, 2026
Subsetting scConcept embeddings Open

Difficulty 4/5 3-5 days Newbie friendliness 35/100

theislab/scConcept#22 · Opened Jun 16, 2026
Installation Instruction Open

bug

Difficulty 2/5 1-3 hours Newbie friendliness 45/100

theislab/embpy#35 · Opened Jun 15, 2026
Request: Chinese translation mirror for single-cell best practices Open

theislab/single-cell-best-practices#447 · 13 comments · 2 assignees · Opened Jun 13, 2026
scConcept models as safetensors Open

Difficulty 3/5 1-2 days Newbie friendliness 52/100

theislab/scConcept#21 · 1 comment · Opened Jun 8, 2026
add blablador models Open

enhancement

Difficulty 4/5 3-5 days Newbie friendliness 35/100

theislab/embpy#34 · Opened Jun 8, 2026
ott-jax incompatible with JAX >= 0.9 (is_vmappable removed) — online/batched OT broken Open

Difficulty 2/5 1-3 hours Newbie friendliness 68/100

theislab/moscot#842 · 1 comment · Opened Jun 5, 2026
Define Tranformations for Coupling data. Open

enhancement good first issue

Difficulty 4/5 3-5 days Newbie friendliness 35/100

theislab/sckitflow#106 · Opened Jun 4, 2026
Consider the application of transformations by default. Open

enhancement help wanted question

Difficulty 5/5 Over a week Newbie friendliness 25/100

theislab/sckitflow#105 · Opened Jun 4, 2026
Missing environment in IR chapter Open

Difficulty 2/5 1-3 hours Newbie friendliness 48/100

theislab/single-cell-best-practices#439 · 1 comment · Opened Jun 1, 2026
Allow sampling all nodes in the `Sampler` class. Open

enhancement good first issue

theislab/sckitflow#104 · 1 assignee · Opened May 28, 2026
Allow arbitrary maximum time for sampling in `CFM`. Open

enhancement good first issue

theislab/sckitflow#103 · 1 assignee · Opened May 28, 2026
Allow batching predictions over nodes. Open

enhancement good first issue

theislab/sckitflow#102 · 1 assignee · Opened May 26, 2026
Allow prediction without target states Open

enhancement question

theislab/sckitflow#101 · 1 comment · 2 assignees · Opened May 26, 2026
Alternative prediction strategy with continuous condition covariates and controls Open

enhancement good first issue

Difficulty 4/5 3-5 days Newbie friendliness 35/100

theislab/sckitflow#87 · Opened May 21, 2026
Build the Docs Open

documentation enhancement

Difficulty 5/5 Over a week Newbie friendliness 20/100

theislab/sckitflow#86 · Opened May 21, 2026
Rebase `torchax-impl` and `torchax-impl-tutorials` branches Open

bug enhancement help wanted question

Difficulty 3/5 1-2 days Newbie friendliness 25/100

theislab/sckitflow#85 · Opened May 21, 2026
Fix CI tests Open

bug good first issue

theislab/sckitflow#80 · 1 comment · 1 assignee · Opened May 20, 2026

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