theislab/scib

Issues

• Test CCA integration with scib

  #419 opened 2 months ago by mairamirza
  1

• Graph iLISI gives a super low score for well-integrated data

  #418 opened 2 months ago by dariotommasini
  0

• Incosistent usage of adata.copy() argument in integration.py

  #417 opened 3 months ago by vondoRishi
  0

• export the benchmarking table resuls as pdf

  #416 opened 3 months ago by mohamednhassan
  0

• kBET metrics does not work with scipy==1.14.0

  #412 opened 4 months ago by kollo97
  1

• Lisi Installation Failed

  #413 opened 4 months ago by srupendra
  1

• Computing Metrics on Seurat Objects

  #411 opened 4 months ago by VishD17
  0

• scanorama does not subset to HVG list

  #382 opened 2 years ago by mbuttner
  1

• scib import failure with scanpy 1.10.0

  #401 opened 8 months ago by mmdanziger
  2

• Questions about the weighted score design of scIB

  #391 opened a year ago by HelloWorldLTY
  1

• how to merge and integrate the TPM and raw counts matrix data

  #387 opened a year ago by Teich2233
  1

• No such file or directory: '/tmp/lisi_gtjq4lmu/graph_lisi_indices_0.txt'

  #386 opened 8 months ago by BillyChen123
  2

• where can i download the benchmarking data ？ Please

  #398 opened 8 months ago by noob000007
  1

• 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")"

  #399 opened 8 months ago by NicoNiCoN11
  1

• Question on Benchmarking Cell Type Assignments Post-Integration and Concerns about Bias in Results

  #393 opened a year ago by MariaRosariaNucera
  2

• scib.metrics.metrics returns all NaN

  #400 opened 8 months ago by Jiayi-Zheng
  0

• Can "Scib" evaluate the integration functionality of Seurat v5 ?

  #397 opened 10 months ago by zhangmiaomiao379
  0

• Metrics fail when there are unused labels

  #379 opened 2 years ago by lazappi
  1

• mertric about ASW

  #392 opened a year ago by BillyChen123
  0

• use_rep in cluster_optimal_resolution and opt_louvain

  #389 opened a year ago by kzkedzierska
  0

• AttributeError: can't set attribute 'categories'

  #388 opened a year ago by BillyChen123
  0

• Error runing LISI when reading index file

  #374 opened a year ago by HelloWorldLTY
  5

• Running scib.metrics.metrics() produces dataframe of NaNs

  #385 opened a year ago by EvanDMee
  1

• Comparing metrics from different embeddings

  #384 opened a year ago by samfenske
  0

• Possibility to report the cLISI score for each cluster?

  #383 opened a year ago by auesro
  0

• FileNotFoundError when running ilisi metric

  #375 opened 2 years ago by katelynxli
  3

• Question on publicly available reprocessed datasets

  #378 opened 2 years ago by kostaslazaros
  1

• louvain deprecation

  #360 opened 2 years ago by deniskristak
  3

• Error reading LISI index file

  #376 opened 2 years ago by lazappi
  2

• Missing documentation for `cluster_optimal_resolution()`

  #365 opened 2 years ago by lazappi
  0

• `cluster_optimal_resolution()` assumes argument order which can be incorrect for asymmetric metrics

  #366 opened 2 years ago by lazappi
  1

• isolated label scores do not return expected results

  #367 opened 2 years ago by danielStrobl
  1

• Add perfect score metric tests for isolated labels

  #359 opened 2 years ago by LuckyMD
  2

• Update integration methods

  #363 opened 2 years ago by mumichae
  0

• AttributeError: Can only use .cat accessor with a 'category' dtype (when running lisi() metric)

  #358 opened 2 years ago by FZ-hajji
  3

• ilisi_graph error

  #357 opened 2 years ago by kostaslazaros
  3

• scib.me.ilisi_graph: FileNotFoundError: [Errno 2] No such file or directory: '/tmp/lisi_svo3el2i/graph_lisi_indices_0.txt'

  #333 opened 2 years ago by guott15
  5

• Preprocessing best practices, scvi wrapper usage, anndata inputs to scib.metrics

  #355 opened 2 years ago by dana-mcc
  0

• Cannot understand the mean of scib.metrics.pcr_comparison parameter

  #348 opened 2 years ago by houruiyan
  1

• GPU support for scib metrics?

  #352 opened 2 years ago by AaronNing
  2

• `cell_cycle` returns poor scores on perfect data input

  #351 opened 2 years ago by scottgigante-immunai
  4

• Not really able to import scib

  #353 opened 2 years ago by das2000sidd
  2

• kBET module not found error is supplanted by an np.nan return

  #349 opened 2 years ago by LuckyMD
  2

• ilisi scores

  #337 opened 2 years ago by aissav
  1

• Running SCIB

  #341 opened 2 years ago by hezarfenfly
  3

• Rpy2 as optional dependency

  #338 opened 2 years ago by mumichae
  0

• Import scib error "but is an incompatible architecture (have 'x86_64', need 'arm64e" MacOXS Monterrey 12.5.1 with Apple M1 ultra

  #332 opened 2 years ago by DRSEI
  2

• Normalize: could not find function "sizeFactors"

  #331 opened 2 years ago by Mari123i
  1

• Missing kBET argument documentation

  #336 opened 2 years ago by lazappi
  0

• Does scgen uses layers.counts or adata.X normalized counts, and where is this indicated?

  #335 opened 2 years ago by ilibarra
  2