General#
The three canonical workflows are compound screens, genetic screens and learned embeddings. This section holds the steps they share: loading data, quality control, normalization, feature analysis, and the pitfalls to watch for.
- scverse.org
-
Core
- AnnData
- decoupler
- MuData
- Muon
- Pertpy
- rapids-singlecell
- Scanpy
- Scirpy
- scvi-tools
- SnapATAC2
- SpatialData
- Squidpy
-
Ecosystem
- AESTETIK
- AlphaPeptTools
- AmbiDose
- annbatch
- anndata for R
- anndataR
- annsel
- AnnZarro
- ATLAS
- benGRN
- bento-tools
- biolord
- cell2location
- Cell_BLAST
- CellAnnotator
- CellCharter
- CellMapper
- CellOracle
- CellphoneDB
- CellRank
- cellxgene
- Cirrocumulus
- clone2vec
- cuspa
- dandelion
- delnx
- DOTools_py
- DoubletDetection
- DRVI
- dvp-io
- dynamo-release
- epiScanpy
- eschr
- fava
- flashdeconv
- flowsom
- GATAC
- GPTBioInsightor
- grassp
- GRnnData
- gssnng
- harpy
- hotspot
- illico
- infercnvpy
- kompot
- LazySlide
- liana
- mantispy
- Marsilea
- maxspin
- moscot
- Mowgli
- Multivelo
- ncountr
- NicheNetPy
- nichepca
- novae
- omicverse
- Palantir
- Panpipes
- ParTIpy
- PathML
- pcdl
- PEAKQC
- pegasus
- PILOT
- popV
- pycea
- pychromVAR
- pyCrossTalkeR
- PyDESeq2
- pyLemur
- pySCENIC
- pytximport
- pyUCell
- Rectangle
- SC2Spa
- SCALEX
- scanpro
- scATrans
- scCellFie
- scDataLoader
- scFair
- scFates
- scGen
- schist
- scib
- scib-metrics
- scib-rapids
- scmcp
- scPRINT
- scPRINT-2
- scTriangulate
- scVelo
- scviva-tools
- scxmatch
- scXpand
- scyan
- sift-sc
- sincei
- Sobolev Alignment
- sopa
- spatial-eggplant
- spatialdataR
- spatialproteomics
- spatiomic
- STMiner
- Symphonypy
- tangram
- TAU Community Detection
- TreeData
- vitessce
- wsidata
- zellkonverter