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Package Usage: pypi: scvi-tools
Deep probabilistic analysis of single-cell omics data.
76 versions
Latest release: 3 months ago
38 dependent packages
24,295 downloads last month
View more package details: https://packages.ecosyste.ms/registries/pypi.org/packages/scvi-tools
View more repository details: https://repos.ecosyste.ms/hosts/GitHub/repositories/scverse%2Fscvi-tools
Dependent Repos 110
BoevaLab/CanSig
Discovering de novo shared transcriptional programs in single cancer cells- * requirements.txt
Size: 5.15 MB - Last synced: 15 days ago - Pushed: 10 months ago
lazappi/openproblems Fork of openproblems-bio/openproblems
Formalizing and benchmarking open problems in single-cell genomics- * docker/openproblems-python-batch-integration/requirements.txt
- ==0.16. docker/openproblems-python-extras/requirements.txt
- * docker/openproblems-python-scvi/requirements.txt
Size: 90.5 MB - Last synced: 9 months ago - Pushed: about 1 year ago
jst-seminar-rostlab-tum/genomics.ai
a web application to annotate and visualise single-cell sequencing data using neural networks- ==0.16.1 Machine_Learning/scarches-api/requirements.txt
Size: 269 MB - Last synced: about 1 year ago - Pushed: almost 2 years ago
theislab/cpa
The Compositional Perturbation Autoencoder (CPA) is a deep generative framework to learn effects of perturbations at the single-cell level. CPA performs OOD predictions of unseen combinations of drugs, learns interpretable embeddings, estimates dose-response curves, and provides uncertainty estimates.- >=0.16.4 pyproject.toml
Size: 54 MB - Last synced: 5 days ago - Pushed: about 2 months ago
MohammedZidane/scarches-cl Fork of theislab/scarches
continual learning for scarches- >=0.12.1 setup.py
Size: 537 MB - Last synced: 2 months ago - Pushed: 7 months ago
bedapub/besca
BESCA (Beyond Single Cell Analysis) offers python functions for single-cell analysis- ==0.15.0 devtools/requirements.txt
- * requirements.txt
Size: 484 MB - Last synced: 7 days ago - Pushed: about 2 months ago
calico/solo
software to detect doublets- * requirements.txt
Size: 36.4 MB - Last synced: 23 days ago - Pushed: 23 days ago
theislab/multigrate
Multigrate: multiomic data integration for single-cell genomics- ^0.14.6 pyproject.toml
Size: 9.69 MB - Last synced: 27 days ago - Pushed: 27 days ago
theislab/scgen
Single cell perturbation prediction- >=0.15.0 pyproject.toml
Size: 69 MB - Last synced: 28 days ago - Pushed: 8 months ago
danielStrobl/SingleCellOpenProblems Fork of openproblems-bio/openproblems
Formalizing and benchmarking open problems in single-cell genomics- * docker/openproblems-r-pytorch/requirements.txt
- * docker/openproblems-python-pytorch/requirements.txt
Size: 77.4 MB - Last synced: 11 months ago - Pushed: about 1 year ago
MartinBanchero/scarches Fork of theislab/scarches
Query to reference mapping for single-cell genomics- >=0.8.0b0 docs/requirements.txt
- >=0.12.1 setup.py
Size: 414 MB - Last synced: 7 months ago - Pushed: over 2 years ago
scverse/scvi-tools-skeleton 📦
Template repository for creating novel models with scvi-tools- >=0.15.0,<0.16.0 pyproject.toml
Size: 75.2 KB - Last synced: about 1 year ago - Pushed: over 1 year ago
menchelab/novarinocollab
A repository containing the code for the collaboration with the Novarino lab- ==0.15.2 environment.yml
Size: 177 MB - Last synced: 7 months ago - Pushed: 7 months ago
BiomedicalMachineLearning/Medulloblastoma
- ==0.12.0 requirements.txt
Size: 12.9 MB - Last synced: 14 days ago - Pushed: about 1 year ago
YosefLab/velovi
- >=0.16.4 pyproject.toml
Size: 659 KB - Last synced: 13 days ago - Pushed: 13 days ago
openproblems-bio/openproblems
Formalizing and benchmarking open problems in single-cell genomics- * docker/openproblems-r-pytorch/requirements.txt
- * docker/openproblems-python-pytorch/requirements.txt
Size: 73.1 MB - Last synced: 13 days ago - Pushed: 4 months ago
LucasESBS/vega
VEGA: VAE Enhanced by Gene Annotations- 0.9.0 poetry.lock
- 0.9.0 pyproject.toml
Size: 26.1 MB - Last synced: 17 days ago - Pushed: about 2 years ago
theislab/scarches
Reference mapping for single-cell genomics- >=0.12.1 setup.py
Size: 784 MB - Last synced: 12 days ago - Pushed: about 2 months ago
WormBase/wormcells-viz
Visualization tools for C. elegans single cell RNA sequencing data- * requirements.txt
Size: 504 KB - Last synced: 6 months ago - Pushed: 6 months ago
WormBase/scdefg
A single page Flask app with a GUI for performing differential expression with scvi-tools. Returns a volcano plot and downloadable tables with DE results.- ==0.13.0 requirements.txt
Size: 133 KB - Last synced: about 1 year ago - Pushed: over 1 year ago
Munfred/scdefg
A single page Flask app with a GUI for performing differential expression with scvi-tools. Returns a volcano plot and downloadable tables with DE results.- ==0.11.0 requirements.txt
Size: 136 KB - Last synced: about 1 year ago - Pushed: over 2 years ago
scPolyphony/polyphony
- ==0.14.6 setup.py
Size: 9.49 MB - Last synced: about 1 month ago - Pushed: about 1 year ago
paulgeser/test
- ==0.15.0 devtools/requirements.txt
- * requirements.txt
Size: 292 MB - Last synced: about 1 month ago - Pushed: almost 2 years ago
YosefLab/destvi_utils
Utilities for downstream analysis of destVI- 0.15.4 poetry.lock
Size: 208 KB - Last synced: 9 months ago - Pushed: 9 months ago
fmicompbio/adv_singlecell_2022
Material for the "Advanced topics in single-cell analysis" course (2022 edition)- >=0.16.0 containers/container_jupyter/day3_spatial_transcriptomics/environment.yml
- * containers/container_jupyter/day4_deep_generative_networks/environment.yml
- >=0.16.0 containers/container_rstudio/day3_spatial_transcriptomics/environment.yml
- >=0.15.4 containers/container_rstudio/day3_spatial_transcriptomics/requirements.txt
- * containers/container_rstudio/day4_deep_generative_networks/environment.yml
Size: 274 MB - Last synced: 2 months ago - Pushed: about 2 years ago
mdmanurung/integratune 📦
- 0.16.4 poetry.lock
- ^0.16.4 pyproject.toml
Size: 804 KB - Last synced: about 1 year ago - Pushed: over 1 year ago
EmanuelSoda/Docker
Repo for all my Docker images- ==0.17.3 singel_cell_notebook/requirements.txt
Size: 21.5 KB - Last synced: about 1 year ago - Pushed: over 1 year ago
yezhengSTAT/scVI-3D
- >=0.14.5 python-requirements.txt
Size: 77.7 MB - Last synced: 8 days ago - Pushed: 9 days ago
theislab/scatac_poisson_reproducibility
- * setup.py
Size: 192 MB - Last synced: 6 months ago - Pushed: 6 months ago
j-germino/scrnatools-git
Helper methods for scRNAseq processing using scanpy + scVI- * setup.py
Size: 25.1 MB - Last synced: 9 months ago - Pushed: 9 months ago
YosefLab/mrvi_archive
Multi-resolution Variational Inference- >=0.17.0 pyproject.toml
Size: 73.2 KB - Last synced: 27 days ago - Pushed: 27 days ago
bucky527/scME
- ==0.19.0 environment.yaml
Size: 20.8 MB - Last synced: about 1 year ago - Pushed: over 1 year ago
theislab/scarches-1 Fork of theislab/scarches
Reference mapping for single-cell genomics- >=0.12.1 setup.py
Size: 582 MB - Last synced: 7 months ago - Pushed: 7 months ago
DendrouLab/panpipes
Multi-modal single cell analysis pipelines- ==0.16.3 requirements.txt
Size: 2.44 MB - Last synced: 17 days ago - Pushed: 17 days ago
schwab-lab/annotateCSF
Python GUI tool for annotation of scRNAseq datasets containing CSF immune cells.- ==0.13.0 requirements_linux.txt
- ==0.13.0 requirements_minimal.txt
- ==0.13.0 requirements_win.txt
Size: 25.5 MB - Last synced: 7 months ago - Pushed: 7 months ago
VergaJU/BoneMarrow_scRNA-Seq
Collection of scripts, pipelines and files used to create a new dataset of scRNA-Seq data.- ==0.16.2 Batch-correct/container/requirements.txt
Size: 95.9 MB - Last synced: 8 months ago - Pushed: 8 months ago
giovp/SingleCellOpenProblems Fork of openproblems-bio/openproblems
Formalizing and benchmarking open problems in single-cell genomics- * docker/openproblems-python-batch-integration/requirements.txt
- ==0.16. docker/openproblems-python-extras/requirements.txt
- * docker/openproblems-python-scvi/requirements.txt
Size: 90.1 MB - Last synced: about 1 month ago - Pushed: 9 months ago
dbdimitrov/openproblems Fork of openproblems-bio/openproblems
Formalizing and benchmarking open problems in single-cell genomics- * docker/openproblems-python-batch-integration/requirements.txt
- * docker/openproblems-python-scvi/requirements.txt
Size: 78.1 MB - Last synced: about 1 year ago - Pushed: about 1 year ago
gabnasello/sc-py-env
Docker Image for scRNA-seq data analysis with Python- * requirements.txt
Size: 14.6 KB - Last synced: 10 days ago - Pushed: 11 days ago
wes-lewis/SingleCellOpenProblems Fork of openproblems-bio/openproblems
Formalizing and benchmarking open problems in single-cell genomics- * docker/openproblems-python-pytorch/requirements.txt
- * docker/openproblems-r-pytorch/requirements.txt
Size: 90.8 MB - Last synced: about 1 year ago - Pushed: over 1 year ago
BoevaLab/CanSig-Supplementary-Information
This repository supplements the CanSig tool (https://github.com/boevaLab/cansig), providing additional information on performed experiments.- * benchmark/requirements.txt
Size: 29.8 MB - Last synced: 15 days ago - Pushed: about 1 year ago
Genentech/sVAE
- ==0.18.0 pyproject.toml
Size: 1.54 MB - Last synced: 5 months ago - Pushed: 10 months ago
LuckyMD/SingleCellOpenProblems Fork of openproblems-bio/openproblems
Formalizing and benchmarking open problems in single-cell genomics- * docker/openproblems-python-batch-integration/requirements.txt
- * docker/openproblems-python-scvi/requirements.txt
Size: 76.3 MB - Last synced: about 1 year ago - Pushed: about 1 year ago
vitkl/openproblems Fork of openproblems-bio/openproblems
Formalizing and benchmarking open problems in single-cell genomics- * docker/openproblems-python-batch-integration/requirements.txt
- ==0.16. docker/openproblems-python-extras/requirements.txt
- * docker/openproblems-python-scvi/requirements.txt
Size: 72.6 MB - Last synced: about 1 year ago - Pushed: over 1 year ago
mxposed/SingleCellOpenProblems Fork of openproblems-bio/openproblems
Formalizing and benchmarking open problems in single-cell genomics- * docker/openproblems-python-pytorch/requirements.txt
- * docker/openproblems-r-pytorch/requirements.txt
Size: 90.5 MB - Last synced: about 1 month ago - Pushed: about 1 year ago
scottgigante-immunai/openproblems Fork of openproblems-bio/openproblems
Formalizing and benchmarking open problems in single-cell genomics- * docker/openproblems-python-batch-integration/requirements.txt
- ==0.16. docker/openproblems-python-extras/requirements.txt
- * docker/openproblems-python-scvi/requirements.txt
Size: 73 MB - Last synced: about 1 year ago - Pushed: about 1 year ago
cameronraysmith/pyrovelocity Fork of pinellolab/pyrovelocity
- 0.13.0 poetry.lock
Size: 168 MB - Last synced: about 1 month ago - Pushed: about 2 months ago
pnm27/snRNA_scRNA_Pipeline
Snakemake Pipeline with "selectable" modules- =0.12.1=pypi_0 requirements/requirements_conda.txt
- ==0.12.1 requirements/requirements_pip.txt
Size: 9.99 MB - Last synced: 26 days ago - Pushed: 26 days ago
MarioniLab/oor_benchmark
A sandbox for benchmarking detection of out-of-reference cells in single-cell genomics data- * docs/requirements.txt
- * pyproject.toml
Size: 453 KB - Last synced: 5 months ago - Pushed: 5 months ago
bowang-lab/scFormer
- 0.16.4 poetry.lock
- ^0.16.0 pyproject.toml
- * requirements.txt
Size: 1.37 MB - Last synced: about 1 year ago - Pushed: over 1 year ago
cellgeni/jupyter-images
Cellular Genetics Informatics Docker Images for Jupyter- * images/full/environment.yml
- * images/python/environment.yml
Size: 109 KB - Last synced: 4 days ago - Pushed: 4 days ago
singha53-zz/gnnomics
- 0.14.5 poetry.lock
- >=0.14.3,<0.15.0 pyproject.toml
Size: 66.9 MB - Last synced: about 1 year ago - Pushed: about 2 years ago
GYQ-form/scBC
scBC —— a single-cell transcriptome Bayesian biClustering framework- >=0.19.0 setup.py
Size: 2.44 MB - Last synced: 4 days ago - Pushed: 2 months ago
scverse/simple-scvi
Simple scVI implementation- >=0.20.1 pyproject.toml
Size: 64.5 KB - Last synced: 27 days ago - Pushed: 27 days ago
ismms-himc/himc_dockers
Docker builds for all tools used by HIMC- >=0.15.3 cell2location/environment.yml
Size: 450 KB - Last synced: about 1 year ago - Pushed: over 1 year ago
GeertvanGeest/scs-docker
Dockerfiles for images hosted at https://hub.docker.com/r/geertvangeest/single_cell_summerschool- * deep_learning/python/requirements.txt
Size: 22.5 KB - Last synced: 10 months ago - Pushed: over 2 years ago
WWXkenmo/scVI_vampPrior
A new scVI model with vampPrior- >=0.15.0,<0.16.0 pyproject.toml
Size: 8.79 KB - Last synced: 10 months ago - Pushed: over 1 year ago
makotu1208/open-problems-multimodal-3rd-solution
open-problems-multimodal-3rd-solution- ==0.17.3 requirements.txt
Size: 261 KB - Last synced: about 1 year ago - Pushed: over 1 year ago
lutrarutra/cellbro
Interactive Single-Cell Analysis Browser- * requirements.txt
Size: 2.9 MB - Last synced: 10 months ago - Pushed: 10 months ago
paulcrowley/scGPT Fork of bowang-lab/scGPT
- ==0.16.4 docs/environment.yml
- ==0.16.4 docs/requirements.txt
- 0.16.4 poetry.lock
- ^0.16.0 pyproject.toml
- ==1.0.2 requirements.txt
Size: 14.7 MB - Last synced: 11 months ago - Pushed: 11 months ago
NKI-CCB/Percolate
Implementation of Percolate, an exponential family JIVE statistical model for multi-view integration- * setup.py
Size: 64.5 KB - Last synced: 13 days ago - Pushed: over 1 year ago
NKI-CCB/sobolev_alignment_manuscript
- ==0.14.4 python_requirements.txt
Size: 5.73 MB - Last synced: 13 days ago - Pushed: about 1 year ago
paulgeser/besca-bfg
- ==0.15.0 devtools/requirements.txt
Size: 257 MB - Last synced: about 1 month ago - Pushed: over 1 year ago