-
recipe
cellrank
Continuous Lineage Decisions Uncovered by RNA Velocity
- Homepage
- Documentation
- License
BSD
- Recipe
CellRank is a toolkit to uncover cellular dynamics based on scRNA-seq data with RNA velocity annotation, see La Manno et al. (2018) and Bergen et al. (2019). CellRank models cellular dynamics as a Markov chain, where transition probabilities are computed based on RNA velocity and transcriptomic similarity, taking into account uncertainty in the velocities.
-
package
cellrank
¶ -
- Versions
1.1.0-0
,1.0.0-0
,1.0.0rc12-0
,1.0.0rc10-0
,1.0.0rc9-0
,1.0.0rc8-0
,1.0.0rc7-0
,1.0.0rc6-0
,1.0.0rc4-0
,1.1.0-0
,1.0.0-0
,1.0.0rc12-0
,1.0.0rc10-0
,1.0.0rc9-0
,1.0.0rc8-0
,1.0.0rc7-0
,1.0.0rc6-0
,1.0.0rc4-0
,1.0.0rc2-0
,1.0.0rc0-0
,1.0.0b3-0
- Depends
anndata
>=0.7.2
docrep
>=0.2.7
ipywidgets
>=7.5.1
joblib
>=0.13.1
matplotlib-base
>=3.3.0
networkx
>=2.2
numba
>=0.51.0
numpy
>=1.19.1
pandas
>=0.23.4
pygam
>=0.8.0
python
>=3.6
scanpy
>=1.5.1
scikit-learn
>=0.21.3
scipy
>=1.2.0
scvelo
>=0.2.1
seaborn
>=0.10.0
setuptools
>=41.0.1
tzlocal
>=1.5.1
wrapt
>=1.12.1
- Required By
Installation
With an activated Bioconda channel (see 2. Set up channels), install with:
conda install cellrank
and update with:
conda update cellrank
or use the docker container:
docker pull quay.io/biocontainers/cellrank:<tag>
(see cellrank/tags for valid values for
<tag>
)
-
package
cellrank-krylov
¶ -
- Versions
1.1.0-0
,1.0.0-0
,1.0.0rc12-0
,1.0.0rc10-0
,1.0.0rc9-0
,1.0.0rc8-0
,1.0.0rc7-0
,1.0.0rc6-0
,1.0.0rc4-0
,1.1.0-0
,1.0.0-0
,1.0.0rc12-0
,1.0.0rc10-0
,1.0.0rc9-0
,1.0.0rc8-0
,1.0.0rc7-0
,1.0.0rc6-0
,1.0.0rc4-0
,1.0.0rc2-0
,1.0.0rc0-0
- Depends
- Required By
Installation
With an activated Bioconda channel (see 2. Set up channels), install with:
conda install cellrank-krylov
and update with:
conda update cellrank-krylov
or use the docker container:
docker pull quay.io/biocontainers/cellrank-krylov:<tag>
(see cellrank-krylov/tags for valid values for
<tag>
)
Link to this page¶
Render an badge with the following MarkDown:
[](http://bioconda.github.io/recipes/cellrank/README.html)