Ecosyste.ms: Issues

An open API service for providing issue and pull request metadata for open source projects.

GitHub / theislab/scib issues and pull requests

#422 - Bump version: 1.1.6 → 1.1.7

Pull Request - State: closed - Opened by mumichae about 1 month ago - 1 comment

#421 - Extend cell cycle gene scoring

Pull Request - State: closed - Opened by mumichae about 1 month ago - 1 comment

#420 - Fix kBET test for 1.1.6

Pull Request - State: closed - Opened by mumichae 3 months ago - 1 comment

#419 - Test CCA integration with scib

Issue - State: open - Opened by mairamirza 5 months ago - 1 comment

#416 - export the benchmarking table resuls as pdf

Issue - State: open - Opened by mohamednhassan 6 months ago

#415 - Bump actions/download-artifact from 3 to 4.1.7 in /.github/workflows

Pull Request - State: closed - Opened by dependabot[bot] 6 months ago - 1 comment
Labels: dependencies

#414 - Fix lint

Pull Request - State: closed - Opened by mumichae 7 months ago

#413 - Lisi Installation Failed

Issue - State: open - Opened by srupendra 7 months ago - 1 comment

#412 - kBET metrics does not work with scipy==1.14.0

Issue - State: open - Opened by kollo97 7 months ago - 1 comment

#411 - Computing Metrics on Seurat Objects

Issue - State: open - Opened by VishD17 7 months ago

#410 - M.A might not be available, you should use M.toarray()

Pull Request - State: closed - Opened by Zhongzheng99 8 months ago - 2 comments

#409 - Update python-igraph dependency to igraph

Pull Request - State: closed - Opened by szhorvat 9 months ago

#408 - Optimise PC regression

Pull Request - State: closed - Opened by mumichae 10 months ago - 1 comment

#407 - Update codecov with token

Pull Request - State: closed - Opened by mumichae 10 months ago

#406 - Use precomputed clustering

Pull Request - State: closed - Opened by mumichae 10 months ago - 1 comment

#405 - Use `scib.cl.cluster_optimal_resolution` in metrics wrapper

Pull Request - State: closed - Opened by mumichae 11 months ago - 1 comment

#404 - Fix argument deprecation

Pull Request - State: closed - Opened by mumichae 11 months ago - 1 comment

#403 - support scanpy 1.10

Pull Request - State: closed - Opened by martinkim0 11 months ago - 2 comments

#402 - Ensure essential packages are not detached!

Pull Request - State: closed - Opened by zhongzheng1999 11 months ago - 1 comment

#401 - scib import failure with scanpy 1.10.0

Issue - State: closed - Opened by mmdanziger 11 months ago - 2 comments

#400 - scib.metrics.metrics returns all NaN

Issue - State: open - Opened by Jiayi-Zheng 11 months ago

#398 - where can i download the benchmarking data ？ Please

Issue - State: closed - Opened by Xyihang about 1 year ago - 1 comment

#396 - Update dependencies

Pull Request - State: closed - Opened by mumichae about 1 year ago - 1 comment

#395 - Refactor LISI metrics

Pull Request - State: closed - Opened by mumichae about 1 year ago - 1 comment

#394 - Skip labels before loop

Pull Request - State: closed - Opened by johnarevalo about 1 year ago - 3 comments

#392 - mertric about ASW

Issue - State: open - Opened by BillyChen123 about 1 year ago

#391 - Questions about the weighted score design of scIB

Issue - State: open - Opened by HelloWorldLTY about 1 year ago - 1 comment

#390 - fix: check file empty

Pull Request - State: closed - Opened by chyroc about 1 year ago - 1 comment

#388 - AttributeError: can't set attribute 'categories'

Issue - State: open - Opened by BillyChen123 over 1 year ago

#387 - how to merge and integrate the TPM and raw counts matrix data

Issue - State: open - Opened by Teich2233 over 1 year ago - 1 comment

#386 - No such file or directory: '/tmp/lisi_gtjq4lmu/graph_lisi_indices_0.txt'

Issue - State: closed - Opened by BillyChen123 over 1 year ago - 2 comments

#382 - scanorama does not subset to HVG list

Issue - State: open - Opened by mbuttner almost 2 years ago - 1 comment

#381 - provide number of columns to `pd.read_table`

Pull Request - State: closed - Opened by johnarevalo almost 2 years ago - 1 comment

#380 - Set names when reading LISI CSV files

Pull Request - State: open - Opened by lazappi almost 2 years ago - 1 comment

#379 - Metrics fail when there are unused labels

Issue - State: open - Opened by lazappi almost 2 years ago - 1 comment

#378 - Question on publicly available reprocessed datasets

Issue - State: closed - Opened by kostaslazaros almost 2 years ago - 1 comment

#377 - more readable PCA computation and info retrieval

Pull Request - State: closed - Opened by mumichae almost 2 years ago - 1 comment

#376 - Error reading LISI index file

Issue - State: closed - Opened by lazappi about 2 years ago - 2 comments

#375 - FileNotFoundError when running ilisi metric

Issue - State: closed - Opened by katelynxli about 2 years ago - 3 comments
Labels: duplicate

#374 - Error runing LISI when reading index file

Issue - State: open - Opened by HelloWorldLTY about 2 years ago - 5 comments

#373 - Update documentation clustering

Pull Request - State: closed - Opened by mumichae about 2 years ago - 1 comment

#372 - Add GPU_id param for DESC

Pull Request - State: closed - Opened by johnarevalo about 2 years ago - 1 comment

#371 - Scale isolated label ASW

Pull Request - State: closed - Opened by mumichae about 2 years ago - 2 comments

#370 - Run iso label as discussed on friday

Pull Request - State: closed - Opened by danielStrobl about 2 years ago - 1 comment

#369 - Update test_isolated_label.py

Pull Request - State: closed - Opened by danielStrobl about 2 years ago - 2 comments

#368 - Update isolated_labels.py

Pull Request - State: closed - Opened by danielStrobl about 2 years ago - 5 comments

#367 - isolated label scores do not return expected results

Issue - State: closed - Opened by danielStrobl about 2 years ago - 1 comment

#365 - Missing documentation for `cluster_optimal_resolution()`

Issue - State: closed - Opened by lazappi about 2 years ago

#364 - Fix PCA regression error for sparse matrices

Pull Request - State: closed - Opened by mumichae about 2 years ago - 1 comment

#363 - Update integration methods

Issue - State: open - Opened by mumichae about 2 years ago

#362 - Add perfect isolabel ASW test

Pull Request - State: closed - Opened by mumichae about 2 years ago - 3 comments

#361 - Make louvain an optional dependency

Pull Request - State: closed - Opened by mumichae about 2 years ago - 1 comment

#360 - louvain deprecation

Issue - State: closed - Opened by deniskristak about 2 years ago - 3 comments

#359 - Add perfect score metric tests for isolated labels

Issue - State: closed - Opened by LuckyMD about 2 years ago - 2 comments

#357 - ilisi_graph error

Issue - State: closed - Opened by kostaslazaros about 2 years ago - 3 comments

#356 - Fix sc best practices link

Pull Request - State: closed - Opened by mumichae about 2 years ago - 1 comment

#354 - add deprecation decorator for asw_batch

Pull Request - State: closed - Opened by mumichae about 2 years ago - 1 comment

#353 - Not really able to import scib

Issue - State: closed - Opened by das2000sidd about 2 years ago - 2 comments

#352 - GPU support for scib metrics?

Issue - State: closed - Opened by AaronNing about 2 years ago - 2 comments

#351 - `cell_cycle` returns poor scores on perfect data input

Issue - State: open - Opened by scottgigante-immunai about 2 years ago - 4 comments

#350 - Fix kBET import issue

Pull Request - State: closed - Opened by mumichae about 2 years ago - 3 comments

#349 - kBET module not found error is supplanted by an np.nan return

Issue - State: closed - Opened by LuckyMD over 2 years ago - 2 comments

#348 - Cannot understand the mean of scib.metrics.pcr_comparison parameter

Issue - State: closed - Opened by houruiyan over 2 years ago - 1 comment

#347 - Fix code coverage

Pull Request - State: closed - Opened by mumichae over 2 years ago

#346 - Update louvain to 0.8

Pull Request - State: closed - Opened by scottgigante-immunai over 2 years ago - 4 comments

#345 - Only pass max_epochs to SCVI.train if set

Pull Request - State: closed - Opened by scottgigante-immunai over 2 years ago - 1 comment

#344 - Update trVAE 1.1.2

Pull Request - State: open - Opened by mumichae over 2 years ago - 1 comment

#343 - General optimised clustering function

Pull Request - State: closed - Opened by mumichae over 2 years ago - 1 comment

#342 - Fix batch silhouette bug

Pull Request - State: closed - Opened by mumichae over 2 years ago - 1 comment

#341 - Running SCIB

Issue - State: closed - Opened by hezarfenfly over 2 years ago - 3 comments
Labels: question

#340 - Update louvain call to a more recent method

Pull Request - State: closed - Opened by johnarevalo over 2 years ago - 2 comments

#339 - Make rpy2 and anndata2ri optional

Pull Request - State: closed - Opened by mumichae over 2 years ago - 4 comments

#338 - Rpy2 as optional dependency

Issue - State: closed - Opened by mumichae over 2 years ago

#337 - ilisi scores

Issue - State: closed - Opened by aissav over 2 years ago - 1 comment

#336 - Missing kBET argument documentation

Issue - State: open - Opened by lazappi over 2 years ago

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

Issue - State: closed - Opened by ilibarra over 2 years ago - 2 comments
Labels: question

#334 - Bump rp2y dependency

Pull Request - State: closed - Opened by mumichae over 2 years ago - 5 comments

#331 - Normalize: could not find function "sizeFactors"

Issue - State: closed - Opened by Mari123i over 2 years ago - 1 comment

#330 - error when running fast metrics

Issue - State: closed - Opened by littleju714 over 2 years ago - 2 comments
Labels: bug

#329 - Low values for iLISI score

Issue - State: open - Opened by Mari123i over 2 years ago - 1 comment

#328 - Graph connectivities metric

Issue - State: closed - Opened by Chengwei94 over 2 years ago - 1 comment

#327 - Fix scanvi bug

Pull Request - State: closed - Opened by mumichae over 2 years ago - 3 comments

#326 - Fix deprecation warning

Pull Request - State: closed - Opened by mumichae over 2 years ago - 1 comment

#325 - Plotting functions

Pull Request - State: open - Opened by mumichae over 2 years ago - 6 comments

#324 - SCANVI bug

Issue - State: closed - Opened by adamgayoso over 2 years ago

#323 - PCR with NaN values in obs

Issue - State: closed - Opened by Mari123i over 2 years ago - 1 comment

#322 - Bump rpy2 version?

Issue - State: closed - Opened by lazappi over 2 years ago - 1 comment

#321 - scaling per batch, low number of cells

Issue - State: closed - Opened by jayypaul over 2 years ago - 5 comments
Labels: question

#320 - Import Error

Issue - State: closed - Opened by liujilei156231 over 2 years ago