bedapub/besca issues and pull requests

#261 - 260 homologs folder is not installed

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

#260 - homologs folder is not installed

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

#259 - Bump joblib from 1.1.0 to 1.2.0 in /devtools

Pull Request - State: closed - Opened by dependabot[bot] about 2 years ago
Labels: dependencies

#258 - Bump protobuf from 3.19.4 to 3.19.5 in /devtools

Pull Request - State: closed - Opened by dependabot[bot] about 2 years ago
Labels: dependencies

#257 - Bump oauthlib from 3.2.0 to 3.2.1 in /devtools

Pull Request - State: closed - Opened by dependabot[bot] about 2 years ago
Labels: dependencies

#256 - Bump mako from 1.1.6 to 1.2.2 in /devtools

Pull Request - State: closed - Opened by dependabot[bot] about 2 years ago
Labels: dependencies

#255 - #252 added matplotlib version to print_software_versions

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

#254 - #253 replace parameter bbbox_inches with bbox_inches

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

#253 - make plots working with matplotlib >= 3.6

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

#252 - Add matplotlib version to bc.print_software_versions()

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

#251 - Some chunks get lost byopening notebooks in JupyterLab (instead of classical Jupyter notebook)

Issue - State: closed - Opened by hatjek about 2 years ago - 1 comment
Labels: bug

#250 - Std workflow 2.5

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

#249 - Modified mtx read function as fix #167 introduced a bug

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

#248 - Update standard_workflow_besca2.ipynb

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

#247 - 2.5 dev

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

#246 - Fix for issue #176

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

#245 - updated environment.lock.yml

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

#244 - Changed author in setup.py

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

#243 - 217 omit or replace r functions

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

#242 - Fix for issue #100

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

#241 - #240 using random anndata to run test

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

#240 - Download of zenodo fails when running tests

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

#239 - Fix for issue #159

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

#238 - Critical Bug fix: in highly_variable_genes

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

#237 - 12 import functions currently do not check for correct standard formatting

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

#236 - Bump nbconvert from 6.4.2 to 6.5.1 in /devtools

Pull Request - State: closed - Opened by dependabot[bot] about 2 years ago
Labels: dependencies

#235 - Updated Python version

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

#234 - Bug Fix: in commit f6c914a, regress_out was removed and only scaling …

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

#233 - fix bug in bc.pl.dot_heatmap_split

Pull Request - State: closed - Opened by yannik-benndorf about 2 years ago

#232 - Removed double space in Neutro signature (between FCGR3B and CXCR2)

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

#231 - Bump mistune from 0.8.4 to 2.0.3 in /devtools

Pull Request - State: closed - Opened by dependabot[bot] about 2 years ago
Labels: dependencies

#230 - Added check for var_names in citeseq part of sw fixing #149

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

#228 - Request new module on our sHPC with Python 3.9

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

#227 - #167 added a replace after reading in metadata.tsv

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

#226 - Updated python version

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

#225 - 197 the r code in function valoutlier needs modification

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

#224 - 185 bcplupdate qualitative palette is not working proprely

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

#223 - re-factored update_qualitative_palette to work with the category orde…

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

#222 - replaced bc.st.regress_out with sc.pp.scale

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

#221 - Besca issue#3

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

#218 - Compile the documentation for release 2.5

Issue - State: closed - Opened by hatjek over 2 years ago
Labels: documentation

#217 - Omit or replace R functions

Issue - State: closed - Opened by hatjek over 2 years ago - 3 comments
Labels: enhancement

#216 - Added width/height to plotting functions

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

#215 - Omit the regressOut step

Issue - State: closed - Opened by hatjek over 2 years ago
Labels: std workflow

#213 - fixed typo / resolve #187

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

#212 - modified setup.py

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

#205 - Xtra celltype pcs

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

#204 - README update: python version

Issue - State: closed - Opened by leipnerm over 2 years ago - 5 comments

#197 - The R code in function `valOutlier` needs modification

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

#196 - add 20 new cell types and sorted cell type list

Pull Request - State: closed - Opened by schmucr1 over 2 years ago - 1 comment

#185 - bc.pl.update_qualitative_palette is not working proprely

Issue - State: closed - Opened by ajulienla almost 3 years ago - 2 comments
Labels: bug, for future

#183 - allow compressed raw files

Pull Request - State: closed - Opened by schmucr1 almost 3 years ago - 1 comment

#176 - Cleaning up a git repo for reducing the repository size

Issue - State: closed - Opened by hatjek almost 3 years ago - 6 comments
Labels: enhancement, on hold

#173 - fixed typo in preamble

Pull Request - State: closed - Opened by luiswyss about 3 years ago

#167 - Spaces in barcode index result in export inconsistencies and MongoDB errors

Issue - State: closed - Opened by llumdi about 3 years ago - 2 comments
Labels: bug, std workflow

#161 - Documentation for citeseq workflow missing

Issue - State: open - Opened by llumdi over 3 years ago - 4 comments
Labels: documentation, enhancement

#159 - When citeseq = False, reading matrix should load 'gex_only'

Issue - State: closed - Opened by llumdi over 3 years ago - 6 comments
Labels: bug

#155 - Suggestion to also keep signatures with 1 gene

Issue - State: closed - Opened by llumdi over 3 years ago - 1 comment
Labels: question

#154 - errors using sys

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

#149 - cite-seq processing error standard workflow

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

#144 - Issue with R_HOME in standard workflow: ValueError: openrlib.R_HOME cannot be None.

Issue - State: closed - Opened by ajulienla over 3 years ago - 1 comment
Labels: bug

#110 - Cell annotation hierarchy

Issue - State: closed - Opened by swalpe almost 4 years ago - 3 comments
Labels: enhancement

#100 - auto-annot training

Issue - State: closed - Opened by swalpe about 4 years ago - 3 comments
Labels: bug

#74 - Bug in bc.pl.dot_heatmap_split

Issue - State: closed - Opened by ajulienla about 4 years ago
Labels: bug

#62 - FIxing issue in combined_signature_score

Issue - State: closed - Opened by ajulienla about 4 years ago - 1 comment
Labels: bug

#12 - Import functions currently do not check for correct standard formatting

Issue - State: closed - Opened by sophiamaedler over 4 years ago - 13 comments
Labels: help wanted

#3 - Modularized celltype labelling

Issue - State: closed - Opened by ajulienla over 4 years ago - 1 comment
Labels: enhancement, good first issue

GitHub / bedapub/besca issues and pull requests