theislab/scib-pipeline
Snakemake pipeline that works with the scIB package to benchmark data integration methods.
PythonMIT
Issues
- 2
- 6
Pandas version conflict in creating environments
#64 opened by ys-lim - 9
Error in rule metrics_single.
#61 opened by zhongzheng1999 - 0
- 0
error in running scanvi integration
#62 opened by olhakholod - 1
Dependency errors with running scib-pipeline.
#60 opened by TheVille415 - 1
- 8
Error in `[[<-`(`*tmp*`, assay, value = assay.data) : [[<- defined for objects of type "S4" only for subclasses of environment
#48 opened by AlinaKurjan - 1
- 3
error when running pipeline with test data
#37 opened by littleju714 - 1
trouble in running the scib-pipeline
#40 opened by huawen-poppy - 2
confuse in adata and adata_int
#57 opened by huawen-poppy - 5
mouse brain dataset is not available?
#43 opened by yuxiaokang-source - 5
failing to run the initial example
#53 opened by deniskristak - 2
igraph version conflict
#55 opened by cdedonno - 3
Submitting SLURM jobs
#51 opened by mumichae - 2
No trajectory output
#47 opened by mumichae - 2
One tool = one environment?
#3 opened by ilibarra - 8
Pipeline can not find data in adata.obs
#49 opened by ccruizm - 1
Error using sparse matrix
#50 opened by mumichae - 11
scvi and other issues?
#46 opened by AlinaKurjan - 4
error running pipeline
#44 opened by littleju714 - 10
from_scvi_model
#41 opened by cdiaz45 - 1
- 3
error goes with test data
#38 opened by littleju714 - 2
- 9
Error when running snakemake
#34 opened by t-nol - 3
- 6
Generated test data not readable
#26 opened by Hrovatin - 9
Setting environnement variables
#33 opened by t-nol - 10
Installation issues that need fixing
#23 opened by LuckyMD - 10
Pipeline works on your test dataset but fails for experimental dataset - ValueError: Bin edges must be unique: array
#30 opened by stemangiola - 10
Issue with the pipeline
#9 opened by szhang99-bu - 2
R 4 support?
#14 opened by bugneville - 0
from SingleCellExperiment to pipeline
#29 opened by stemangiola - 8
TypeError: int() argument must be a string, a bytes-like object or a number, not 'NAType'
#28 opened by stemangiola - 2
- 2
Error Running Pipeline
#17 opened by DylanTom - 2
- 8
- 1
Hi authors
#16 opened by cquzys - 5
data sets available?
#11 opened by zia1138 - 1
Issue with running snakemake
#8 opened by szhang99-bu - 2
Suspected issue with scanpy version
#7 opened by wkopp - 6
KeyError: 'connectivities'
#5 opened by nrclaudio