Ecosyste.ms: Issues

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GitHub / theislab/scarches issues and pull requests

#249 - TypeError: __init__() got an unexpected keyword argument 'n_epochs'

Issue - State: open - Opened by gaoyifei1122 3 months ago - 2 comments

#247 - Python ver docs

Pull Request - State: open - Opened by chelseabright96 3 months ago - 1 comment

#244 - Reproduction issue in treeArches

Issue - State: open - Opened by hansen7 4 months ago

#243 - add trvae Perturbation prediction notebook

Pull Request - State: closed - Opened by chelseabright96 6 months ago - 4 comments

#242 - trvae Perturbation prediction notebook

Pull Request - State: closed - Opened by chelseabright96 6 months ago - 1 comment

#241 - arm64 osx platform not supported?

Issue - State: open - Opened by erzakiev 6 months ago - 2 comments

#240 - Fix gdrive link

Pull Request - State: closed - Opened by chelseabright96 6 months ago - 1 comment

#239 - Can trVAE in scarches be applied to perturbation prediction?

Issue - State: closed - Opened by weizhiting 6 months ago - 2 comments

#238 - fix pbmc gdrive link

Pull Request - State: closed - Opened by chelseabright96 6 months ago - 1 comment

#237 - Specify the number of cores

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

#235 - scGEN network.batch_removal error

Issue - State: closed - Opened by dKlee99 6 months ago - 1 comment

#233 - downgrade gdown to fix permissions error for pbmc_tutorial.h5ad

Pull Request - State: closed - Opened by chelseabright96 8 months ago - 1 comment

#232 - Fix issue #224 / Improve handling of unlabled cells

Pull Request - State: open - Opened by moinfar 8 months ago

#231 - PBMC data no longer available

Issue - State: open - Opened by huananfshi 8 months ago - 7 comments

#230 - Add minification function for scPoli

Pull Request - State: open - Opened by chelseabright96 9 months ago

#229 - No module named 'jax.extend'

Issue - State: closed - Opened by dustin-mullaney 9 months ago - 1 comment

#228 - Issue with expimap model

Issue - State: closed - Opened by MoLuLuMo 9 months ago - 1 comment

#226 - Issue in annotating cell types of unlabelled query data by scPoli

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

#225 - Choice of reference and query data sets

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

#224 - scPoli Model for Unsupervised Use

Issue - State: open - Opened by ShreyParikh07 10 months ago - 1 comment

#223 - Allow pickling from GPU to CPU

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

#222 - More detailed training logs

Issue - State: closed - Opened by Nusob888 11 months ago - 2 comments

#221 - Scpoli get latent

Pull Request - State: closed - Opened by chelseabright96 11 months ago - 1 comment

#220 - scPoli usage

Issue - State: closed - Opened by Nusob888 11 months ago - 4 comments

#219 - environment reproducibility

Issue - State: closed - Opened by racng about 1 year ago - 2 comments

#218 - Speed improvement

Pull Request - State: open - Opened by moinfar about 1 year ago - 2 comments

#217 - Update of conda environment yaml

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

#216 - the difference between scPoli and scANVI

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

#214 - Errors extracting embeddings

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

#213 - hlca_map_classify.ipynb missing early_stopping_kwarg

Issue - State: open - Opened by c-westhoven about 1 year ago

#212 - problems about scHPL training

Issue - State: closed - Opened by YawnC about 1 year ago - 13 comments

#210 - cannot setup.py install

Issue - State: closed - Opened by jianrong0520 about 1 year ago - 7 comments

#209 - scArches for PeakVI

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

#208 - Multiple categorical_covariate_keys not allowed

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

#207 - Perform scArches in R using Seurat

Issue - State: open - Opened by ConDem94 over 1 year ago

#206 - fail to use the sca.models.SCVI

Issue - State: open - Opened by melancholy12 over 1 year ago - 7 comments

#205 - fail to using scpoli for dataset training

Issue - State: closed - Opened by melancholy12 over 1 year ago - 2 comments

#203 - Fail to establish scpoli model

Issue - State: closed - Opened by melancholy12 over 1 year ago - 2 comments

#202 - Fail to import scarches

Issue - State: closed - Opened by melancholy12 over 1 year ago - 2 comments

#201 - fix typo - `condition_key` vs `condition_keys`

Pull Request - State: closed - Opened by maarten-devries over 1 year ago

#198 - Potential bugs for label transfer

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

#197 - Fail to get latent representation of reference + query dataset

Issue - State: closed - Opened by Yuki-YqHuang over 1 year ago - 1 comment

#196 - scPoli dtype error

Issue - State: closed - Opened by JesperGrud over 1 year ago - 4 comments

#195 - Scpoli：RuntimeError: expected scalar type Float but found Double

Issue - State: closed - Opened by melancholy12 over 1 year ago - 1 comment

#194 - Install issue - no .yml in repo

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

#192 - Update index.rst

Pull Request - State: closed - Opened by M0hammadL over 1 year ago

#191 - Mapping and label transfer tutorial rewriting

Pull Request - State: closed - Opened by LisaSikkema over 1 year ago - 1 comment

#190 - Scpoli/dev new

Pull Request - State: closed - Opened by cdedonno over 1 year ago - 1 comment

#189 - Revert "Revert "Scpoli/dev""

Pull Request - State: closed - Opened by M0hammadL over 1 year ago - 2 comments

#188 - Revert "Scpoli/dev"

Pull Request - State: closed - Opened by cdedonno over 1 year ago - 1 comment

#187 - Scpoli/dev

Pull Request - State: closed - Opened by cdedonno over 1 year ago - 2 comments

#185 - Which model should I use for a cell typing task

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

#184 - Documentation website failing to load

Issue - State: closed - Opened by virpatel524 over 1 year ago - 5 comments

#183 - Label transfer code producing different outputs in different environments

Issue - State: open - Opened by LisaSikkema over 1 year ago - 10 comments

#182 - ImportError: cannot import name 'setup_anndata' from 'scvi.data'

Issue - State: open - Opened by besidesme over 1 year ago - 2 comments

#181 - Trouble with expimap -- float values wanted when anndata is in double

Issue - State: closed - Opened by virpatel524 over 1 year ago - 5 comments

#180 - Error: Saved model does not contain original setup inputs.

Issue - State: closed - Opened by dsb66 over 1 year ago - 1 comment

#179 - Have `_validate_var_names` support `csr_matrix`

Pull Request - State: closed - Opened by maarten-devries over 1 year ago - 1 comment

#178 - Update _utils.py

Pull Request - State: closed - Opened by maarten-devries over 1 year ago - 1 comment

#177 - Zero- and one-shot mapping

Pull Request - State: open - Opened by alextopalova almost 2 years ago - 3 comments

#176 - "Model was trained without prototypes" when using a loaded scPoli model

Issue - State: closed - Opened by maarten-devries almost 2 years ago - 8 comments

#175 - Scpoli/partitioned embeddings

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

#174 - scpoli/atac

Pull Request - State: closed - Opened by cdedonno almost 2 years ago

#173 - fix further device specifications

Pull Request - State: closed - Opened by cdedonno almost 2 years ago

#172 - fix device bug

Pull Request - State: closed - Opened by cdedonno almost 2 years ago

#170 - scPoli get latent representations

Issue - State: closed - Opened by melancholy12 almost 2 years ago - 2 comments

#169 - Suggested improvements for label transfer function

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

#167 - WIP scpoli improvements

Pull Request - State: closed - Opened by cdedonno almost 2 years ago

#166 - SageNet tutorial notebook missing one cell for model training

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

#165 - scPoli error of label transfer

Issue - State: closed - Opened by melancholy12 almost 2 years ago - 7 comments

#164 - HLCA notebook

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

#163 - add clarification on pretraining in demo

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

#162 - "get_num_classes" not available in newer torchmetrics versions

Issue - State: open - Opened by NoahMottelson almost 2 years ago - 2 comments

#161 - Matrix multiplication error in scpoli_model.classify

Issue - State: closed - Opened by mariemoullet almost 2 years ago - 13 comments

#160 - For sergei

Pull Request - State: open - Opened by MohammedZidane almost 2 years ago - 4 comments

#159 - For sergei

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

#158 - fix pretraining epoch number and print progress

Pull Request - State: closed - Opened by cdedonno almost 2 years ago

#157 - installation issue

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

#156 - add data link to scpoli demo

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

#155 - Correct the small typo

Pull Request - State: closed - Opened by dineshpalli almost 2 years ago - 2 comments

#154 - scPoli sparse input? (TypeError: 'int' object is not callable)

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

#153 - CUDA error when running scPoli

Issue - State: closed - Opened by DzvinkaYarish almost 2 years ago - 2 comments

#152 - BugFix in scPoli when input anndata has sparse X

Pull Request - State: closed - Opened by moinfar almost 2 years ago

#151 - mvTCR tutorial - Updated Subsampling

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