Ecosyste.ms: Issues

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

GitHub / broadinstitute/CellBender issues and pull requests

#380 - load_anndata_from_input_and_output: retain_input_metadata input to nowhere

Issue - State: open - Opened by benemead about 1 month ago - 2 comments

#379 - high background noise, but really really high!

Issue - State: open - Opened by EEKLUES about 1 month ago

#378 - raw h5ad OR filtered h5ad

Issue - State: open - Opened by elegantmedstu about 1 month ago - 1 comment

#376 - Increased number of UMIs per barcode after running remove-background

Issue - State: closed - Opened by hhvu0102 2 months ago - 1 comment

#375 - CellBender for .BAM file

Issue - State: open - Opened by jzheng25 2 months ago

#373 - Cellbender on multiplexed chemistries

Issue - State: open - Opened by LinearParadox 3 months ago

#372 - Fixed Single cell RNA seq

Issue - State: open - Opened by archana433 3 months ago - 1 comment

#371 - Not saving ckpt.tar.gz checkpoint

Issue - State: open - Opened by IsauraMaria96 3 months ago - 8 comments

#369 - Background Fraction

Issue - State: open - Opened by hk2rma 3 months ago - 2 comments

#368 - v0.3.2

Pull Request - State: closed - Opened by sjfleming 3 months ago

#367 - Azurize CellBender to run on ToA

Pull Request - State: closed - Opened by aawdeh 4 months ago - 5 comments

#366 - Importance of model loss

Issue - State: open - Opened by ShadHOH 4 months ago

#365 - Can't Computing target noise counts per gene for MCKP estimator

Issue - State: open - Opened by Deroline10 4 months ago - 1 comment

#364 - Never mind

Issue - State: closed - Opened by maxwellfinkelstein 4 months ago

#363 - Unhandled division by zero

Issue - State: open - Opened by fm361 4 months ago

#361 - Question about input h5 file

Issue - State: open - Opened by Linxiaobuskiy 4 months ago - 1 comment

#360 - Should I keep decreasing the learning rate?

Issue - State: open - Opened by txemaheredia 4 months ago

#359 - New fileformat output from BD rhapsody

Issue - State: open - Opened by MelanieRN 4 months ago - 1 comment

#354 - How to run CellBender for a pooling library?

Issue - State: open - Opened by tewengtong 5 months ago

#352 - Readme appearance

Pull Request - State: closed - Opened by sjfleming 5 months ago

#351 - Problem installing cellbender

Issue - State: open - Opened by marctormo 5 months ago - 2 comments
Labels: installation

#350 - Fix v0.3.1 bug

Pull Request - State: closed - Opened by sjfleming 6 months ago

#349 - Feature: tool for users to rescue v0.3.1 runs and to re-compute output counts in general

Issue - State: closed - Opened by sjfleming 6 months ago - 1 comment
Labels: enhancement

#348 - HTML output fails due to lxml change

Issue - State: closed - Opened by sjfleming 6 months ago - 6 comments
Labels: bug

#347 - Fix major bug in v0.3.1: negative counts

Pull Request - State: closed - Opened by sjfleming 6 months ago - 3 comments
Labels: bug

#346 - Fix readthedocs

Issue - State: closed - Opened by sjfleming 6 months ago - 1 comment
Labels: bug

#345 - Fix exception loading checkpoint

Pull Request - State: closed - Opened by alecw 6 months ago - 3 comments

#344 - ERROR: Could not build wheels for pyzmq, which is required to install pyproject.toml-based projects

Issue - State: open - Opened by axiba053 6 months ago - 1 comment
Labels: installation

#343 - Index Error in priors.py

Issue - State: open - Opened by Ratoncito 6 months ago - 2 comments
Labels: enhancement

#341 - Changed np.int to np.int64 as the use of np.int is now deprecated

Pull Request - State: closed - Opened by GreenGilad 6 months ago - 1 comment

#340 - Cell Ranger 'Multiplexing Capture' feature type not recognised.

Issue - State: open - Opened by jpintar 7 months ago - 1 comment
Labels: bug

#339 - Update cli.py to add newer Cell Ranger feature types

Pull Request - State: closed - Opened by jpintar 7 months ago - 1 comment

#338 - Problems interpreting results

Issue - State: open - Opened by MarP2606 7 months ago

#337 - CellBender ran successfully but no HTML report generated

Issue - State: open - Opened by wendy0853 7 months ago - 9 comments

#336 - cannot pickle 'weakref.ReferenceType' object

Issue - State: closed - Opened by mousepixels 7 months ago - 1 comment

#334 - Negative raw counts

Issue - State: closed - Opened by IrinaVKuznetsova 7 months ago

#330 - different priors on GPU vs. CPU?

Issue - State: open - Opened by bobermayer 8 months ago

#329 - Crash after completing "Working on chunk (xx / xx)"

Issue - State: open - Opened by Thapeachydude 8 months ago - 4 comments

#328 - No space left on device

Issue - State: open - Opened by IrinaVKuznetsova 8 months ago - 1 comment

#327 - Error generating HTML report?

Issue - State: open - Opened by razorofockham 8 months ago - 2 comments

#326 - Barcode Multiplets

Issue - State: open - Opened by PurwinTJ 8 months ago

#325 - Intepreting nuclei cellbender output

Issue - State: open - Opened by GelatinousGiant 8 months ago

#324 - missing tab/release in GitHub + release on PyPI for v0.3.1

Issue - State: open - Opened by boegel 8 months ago - 2 comments

#323 - ValueError: cannot infer dimensions from zero sized index arrays

Issue - State: open - Opened by OneHitKO 9 months ago - 5 comments

#322 - Cell Bender output pdf file

Issue - State: open - Opened by Seoyeon-Y 9 months ago

#321 - Query: Using CellBender on Multiple scRNA-seq Samples

Issue - State: closed - Opened by ryan2han 9 months ago - 2 comments

#320 - the remove-background data named output.h5 has 0 genes.

Issue - State: open - Opened by Tycooner 9 months ago - 4 comments

#318 - the output.h5 has 0 genes ? it is so strange！

Issue - State: closed - Opened by Tycooner 9 months ago

#317 - Test ELBO higher than train ELBO

Issue - State: open - Opened by ellimarip 9 months ago - 1 comment

#316 - extracting counts data from cellbender/seurat h5

Issue - State: open - Opened by bsmith030465 9 months ago

#315 - Cellbender v.0.3.0 not working with Seurat Read10X_h5 function

Issue - State: open - Opened by smk5g5 10 months ago - 3 comments

#314 - h5ad input

Issue - State: open - Opened by SEVEN-XYCHEN 10 months ago

#313 - Input file

Issue - State: open - Opened by SEVEN-XYCHEN 10 months ago

#312 - Don't crash with ZeroDivisionError if initial test ELBO is the best test ELBO

Pull Request - State: closed - Opened by alecw 10 months ago - 3 comments

#311 - Cellbender paper - UMAPs

Issue - State: open - Opened by dbuszta 10 months ago

#310 - Mitochondrial genes are not removed for NucSeq in v0.3

Issue - State: open - Opened by schmeing 10 months ago - 1 comment

#309 - Different python version

Issue - State: open - Opened by malonzm1 10 months ago

#307 - Selecting specific GPU in multi-GPU environment

Issue - State: open - Opened by Nico995 11 months ago - 1 comment

#306 - negative entries in filtered count matrix?

Issue - State: open - Opened by bobermayer 11 months ago - 7 comments
Labels: bug

#305 - Additional diagnostic plots

Issue - State: open - Opened by wmacnair 11 months ago

#304 - Bump version

Pull Request - State: closed - Opened by sjfleming 11 months ago

#303 - v0.3.1

Pull Request - State: closed - Opened by sjfleming 11 months ago

#302 - Fix bugs with report generation across platforms

Pull Request - State: closed - Opened by sjfleming 11 months ago

#300 - errors writing html file

Issue - State: open - Opened by MengjunWu 11 months ago - 2 comments

#299 - Working with the 'posterior' output - per documentation.

Issue - State: open - Opened by benemead 11 months ago - 8 comments
Labels: enhancement, user question

#296 - TypeError: cannot pickle 'weakref.ReferenceType' object

Issue - State: open - Opened by lili03080317 12 months ago - 13 comments

#295 - CUDA out of memory at MCKP estimator step

Issue - State: open - Opened by Terkild 12 months ago - 4 comments

#293 - ValueError: cannot convert float NaN to integer

Issue - State: open - Opened by sjfleming about 1 year ago
Labels: bug

#290 - save checkpoint to a designated directory?

Issue - State: open - Opened by LiQian-XC about 1 year ago - 5 comments

#289 - cellbender on Crispr guide capture?

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

#287 - Windows no output PDF no output HTML report

Issue - State: open - Opened by sjfleming about 1 year ago - 1 comment
Labels: bug

#286 - The raw counts calculated by cellbender is different from the raw counts of input file

Issue - State: closed - Opened by YiweiNiu about 1 year ago - 2 comments
Labels: user question

#285 - cellbender v0.3.0 failed to remove ambient RNA contamination, what should I do?

Issue - State: closed - Opened by YiweiNiu about 1 year ago - 2 comments
Labels: user question

#284 - Compatibility with 10X Multiome data?

Issue - State: open - Opened by AndiL04 about 1 year ago - 5 comments
Labels: user question

#283 - CellBender Remove-Background: Exploring Hyperparameter Effects

Issue - State: open - Opened by unikill066 about 1 year ago - 2 comments
Labels: user question