rmarkello/abagen issues and pull requests

#237 - For get_expression_data, atlas_info is necessary?

Issue - State: open - Opened by lea231 about 1 month ago

#236 - Error while fetching file 178238387; dataset fetching aborted.

Issue - State: open - Opened by zhengjiezhangtk 2 months ago - 2 comments

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

Pull Request - State: open - Opened by dependabot[bot] 5 months ago
Labels: dependencies

#233 - Assistance Required: Issue with set_axis inplace Parameter in Pandas

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

#232 - AttributeError: 'DataFrame' object has no attribute 'append'

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

#231 - [...] not in index

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

#230 - brain regions from atlas "missing" in expression df

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

#229 - get_expression file does not include all/desired genes

Issue - State: closed - Opened by elosse 11 months ago

#228 - The problem of abagen obtaining the number of AHBA genes

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

#227 - Bug Report: ‘check_surface’ Function Offset Calculation Issue in ‘images.py’

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

#226 - return gene groups in abagen.get_expression_data

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

#225 - DataFrame.set_axis() got an unexpected keyword argument 'inplace' with pandas 2.1.2

Issue - State: closed - Opened by JohannesWiesner over 1 year ago - 12 comments

#224 - Question about atlas

Issue - State: open - Opened by joeyb87 over 1 year ago

#223 - Question about using freesurfer .annot files

Issue - State: closed - Opened by xuansean over 1 year ago - 3 comments

#222 - [DOC] Update docs

Pull Request - State: closed - Opened by liuzhenqi77 over 1 year ago - 1 comment

#221 - [FIX] Fix tests

Pull Request - State: closed - Opened by liuzhenqi77 over 1 year ago

#220 - [FIX] Pandas Compatibility, CI, etc

Pull Request - State: closed - Opened by liuzhenqi77 over 1 year ago

#219 - Fetching aborted when using abagen.get_expression_data

Issue - State: closed - Opened by JohannesWiesner over 1 year ago - 3 comments

#218 - Qustion about the hemisphere filter method in drop_mismatch_samples function (samples_.py L223)

Issue - State: open - Opened by YCHuang0610 over 1 year ago

#217 - get_interpolated_map - Key error for certain genes

Issue - State: closed - Opened by mjmwalsh over 1 year ago

#216 - how to save the expression file?

Issue - State: closed - Opened by qiudashuai1 over 1 year ago - 4 comments

#215 - How to get samples*gene matrix before samples merged in brain region ?

Issue - State: open - Opened by jwli28 almost 2 years ago

#214 - Pandas Compatibility

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

#213 - BUG: TypeError: set_axis() got an unexpected keyword argument 'inplace'

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

#212 - BUG Report: Something wrong with the sample assignment when using Brainnetome atlas(abagen.get_samples_in_mask)

Issue - State: open - Opened by molicaca almost 2 years ago

#211 - BUG Report: Something wrong with the sample assignment when using Brainnetome atlas

Issue - State: closed - Opened by molicaca almost 2 years ago

#210 - Update about using custom parcellation

Issue - State: open - Opened by liuzhenqi77 over 2 years ago

#209 - Question about normalization method before differential expressed gene (DEG) analysis.

Issue - State: closed - Opened by YCHuang0610 over 2 years ago

#208 - Error in running 3.1

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

#207 - Problems downloading microarray data

Issue - State: closed - Opened by njh339 over 2 years ago - 3 comments

#206 - There is a error while add parameter "--ibf_threshold 0.5" in command line

Issue - State: open - Opened by 276562578 over 2 years ago - 1 comment

#205 - How to get expression data based on Destrieux atlas

Issue - State: open - Opened by YH2010 over 2 years ago

#204 - [REF] Replace DataFrame.append with pd.concat

Pull Request - State: closed - Opened by ReinderVosDeWael almost 3 years ago - 2 comments

#203 - Strange sample numbers/`NaN` expression values returned when using text file-based masks/parcellation

Issue - State: open - Opened by alyssadai about 3 years ago - 1 comment

#202 - [DOC] Update abagen citation

Pull Request - State: closed - Opened by rmarkello about 3 years ago - 1 comment

#201 - Bug with tests/mouse/test_gene.py

Issue - State: open - Opened by lonly7star over 3 years ago

#200 - Issue with relabel_gifti?

Issue - State: open - Opened by ik362 over 3 years ago

#199 - [DOC] Adds reference to preprint + updates citation

Pull Request - State: closed - Opened by rmarkello over 3 years ago - 1 comment

#198 - Differential stability values

Issue - State: closed - Opened by gkleinman84 over 3 years ago - 4 comments

#197 - [REF] Handle atlases w/decimal vox sizes

Pull Request - State: closed - Opened by rmarkello over 3 years ago - 1 comment

#196 - the expression results vary greatly with the same atlas at different space resolution.

Issue - State: closed - Opened by Silflame over 3 years ago - 3 comments
Labels: bug

#195 - Cerebellum and Corpus callosum in the included examples atlas (DK)

Issue - State: open - Opened by daedhalus over 3 years ago

#194 - Intensity-based probe filtering for each donor separately

Issue - State: closed - Opened by daedhalus over 3 years ago - 2 comments

#193 - [REF] Re-orient img in `leftify_atlas()`

Pull Request - State: closed - Opened by rmarkello over 3 years ago - 1 comment

#192 - [FIX] Fixes logger error w/reports

Pull Request - State: closed - Opened by rmarkello over 3 years ago - 1 comment

#191 - [FIX] Error with donor-specific atlases and tolerance=0

Pull Request - State: closed - Opened by rmarkello over 3 years ago - 1 comment

#190 - Donor-specific atlases and tolerance=0 fails for two donors

Issue - State: closed - Opened by rmarkello over 3 years ago

#189 - [REF] Fix coordinates of get_samples_in_mask

Pull Request - State: closed - Opened by rmarkello over 3 years ago - 1 comment

#188 - Passing donor masks to `get_samples_in_mask` returns wrong coordinates

Issue - State: closed - Opened by rmarkello over 3 years ago