theislab / scib

Benchmarking analysis of data integration tools

theislab/scib Issues

scib import failure with scanpy 1.10.0
Closed 2 months ago2
Questions about the weighted score design of scIB
Updated 2 months ago1
how to merge and integrate the TPM and raw counts matrix data
Updated 2 months ago1
No such file or directory: '/tmp/lisi_gtjq4lmu/graph_lisi_indices_0.txt'
Closed 2 months ago2
where can i download the benchmarking data ？ Please
Closed 2 months ago1
why the "Unable to allocate 121. GiB for an array with shape (26734, 606219) and data type float64 every time I run "scib.integration.combat(adata, batch= "sample")"
Closed 2 months ago1
Question on Benchmarking Cell Type Assignments Post-Integration and Concerns about Bias in Results
Updated 2 months ago2
scib.metrics.metrics returns all NaN
Updated 3 months ago
Can "Scib" evaluate the integration functionality of Seurat v5 ?
Updated 4 months ago
Metrics fail when there are unused labels
Updated 5 months ago1
mertric about ASW
Updated 6 months ago
use_rep in cluster_optimal_resolution and opt_louvain
Updated 7 months ago
AttributeError: can't set attribute 'categories'
Updated 7 months ago
Error runing LISI when reading index file
Closed 10 months ago5
Running scib.metrics.metrics() produces dataframe of NaNs
Updated a year ago1
Comparing metrics from different embeddings
Updated a year ago
Possibility to report the cLISI score for each cluster?
Updated a year ago
scanorama does not subset to HVG list
Updated a year ago
FileNotFoundError when running ilisi metric
Closed a year ago3
Question on publicly available reprocessed datasets
Closed a year ago1
louvain deprecation
Closed a year ago3
Error reading LISI index file
Closed a year ago2
Low values for iLISI score
Updated a year ago1
Missing documentation for `cluster_optimal_resolution()`
Closed a year ago
`cluster_optimal_resolution()` assumes argument order which can be incorrect for asymmetric metrics
Closed a year ago1
isolated label scores do not return expected results
Closed a year ago1
PCR with NaN values in obs
Closed a year ago1
Add perfect score metric tests for isolated labels
Closed a year ago2
Update integration methods
Updated a year ago
AttributeError: Can only use .cat accessor with a 'category' dtype (when running lisi() metric)
Closed a year ago3
ilisi_graph error
Closed a year ago3
scib.me.ilisi_graph: FileNotFoundError: [Errno 2] No such file or directory: '/tmp/lisi_svo3el2i/graph_lisi_indices_0.txt'
Closed 2 years ago5
Preprocessing best practices, scvi wrapper usage, anndata inputs to scib.metrics
Closed a year ago
Cannot understand the mean of scib.metrics.pcr_comparison parameter
Closed a year ago1
GPU support for scib metrics?
Closed 2 years ago2
`cell_cycle` returns poor scores on perfect data input
Updated 2 years ago4
Not really able to import scib
Closed 2 years ago2
kBET module not found error is supplanted by an np.nan return
Closed 2 years ago2
ilisi scores
Closed 2 years ago1
Running SCIB
Closed 2 years ago3
error when running fast metrics
Closed 2 years ago2
Rpy2 as optional dependency
Closed 2 years ago
Import scib error "but is an incompatible architecture (have 'x86_64', need 'arm64e" MacOXS Monterrey 12.5.1 with Apple M1 ultra
Closed 2 years ago2
Normalize: could not find function "sizeFactors"
Closed 2 years ago1
Missing kBET argument documentation
Updated 2 years ago
Bump rpy2 version?
Closed 2 years ago1
Does scgen uses layers.counts or adata.X normalized counts, and where is this indicated?
Closed 2 years ago2
SCANVI bug
Closed 2 years ago
Graph connectivities metric
Closed 2 years ago1
scaling per batch, low number of cells
Closed 2 years ago5