ebi-gene-expression-group/scanpy-scripts issues and pull requests

#136 - Updating_bats_test

Pull Request - State: open - Opened by anilthanki 3 months ago

#135 - Fixing Scanpy 1.9.3 error for mixed datatype column

Pull Request - State: open - Opened by anilthanki 4 months ago - 2 comments

#134 - Scrublet failing on certain dataset

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

#133 - Move to scanpy 1.9.8

Pull Request - State: open - Opened by pcm32 7 months ago

#132 - Release/v1.9.301 to develop

Pull Request - State: closed - Opened by pcm32 7 months ago - 5 comments

#131 - Release/v1.9.301

Pull Request - State: closed - Opened by pcm32 7 months ago

#130 - HVG genes setting through files

Pull Request - State: closed - Opened by pcm32 8 months ago - 1 comment

#129 - Highly variable genes calculations should allow to blacklist or white list specific subset of genes

Issue - State: open - Opened by pcm32 8 months ago

#128 - Change deprecated sc.read() usages for read_h5ad call

Pull Request - State: closed - Opened by pcm32 8 months ago

#127 - Explain how to update all the way to the Galaxy tools

Pull Request - State: open - Opened by pcm32 8 months ago

#126 - Remove extra pinning for mmnpy

Pull Request - State: closed - Opened by pcm32 8 months ago - 1 comment

#125 - Scrublet double prediction fails with cells with under 5 expressed genes

Issue - State: open - Opened by pcm32 8 months ago

#124 - Scrubblet module fails when running with less than 30 cells

Issue - State: open - Opened by pcm32 11 months ago

#123 - Using a single group in find marker genes fails

Issue - State: open - Opened by pcm32 over 1 year ago

#122 - Add filtering by quantiles

Issue - State: open - Opened by pcm32 over 1 year ago

#121 - PlotEmbedd could give more user friendly errors to allow users to recover

Issue - State: open - Opened by pcm32 over 1 year ago

#120 - What is scanpy-run-umap default for --maxiter INTEGER

Issue - State: closed - Opened by swbioinf almost 2 years ago - 4 comments

#119 - Should we add ability to mark ribosomal genes?

Issue - State: open - Opened by pcm32 almost 2 years ago

#118 - How can I use scanpy_scripts?

Issue - State: open - Opened by cooperist almost 2 years ago - 3 comments

#117 - Move to scanpy 1.9.3 and other improvements

Pull Request - State: closed - Opened by pcm32 about 2 years ago - 8 comments

#116 - Calculations of mito directly generate columns with dtypes that break qc calculations on subsequent filtering

Issue - State: open - Opened by pcm32 about 2 years ago - 3 comments

#115 - Update setup.py to remove t-SNE dependency

Pull Request - State: closed - Opened by pinin4fjords over 2 years ago - 1 comment

#114 - Add compression option to export

Pull Request - State: closed - Opened by pinin4fjords over 2 years ago

#113 - Add Black format checking

Pull Request - State: closed - Opened by pinin4fjords over 2 years ago - 1 comment

#112 - Feature/gzip mtx output

Pull Request - State: closed - Opened by pinin4fjords over 2 years ago - 2 comments

#111 - Feature/unit tests

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

#110 - Add fix for exporting mtx from .raw.X

Pull Request - State: closed - Opened by pinin4fjords almost 3 years ago - 3 comments

#109 - Fix boolean columns during merges of extra info at read time

Pull Request - State: closed - Opened by pinin4fjords about 3 years ago - 3 comments

#108 - Adding fa2 to install so that trajectory tools can use it for setting up the plots

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

#107 - Remove batch handling in favour of scanpy-located code

Pull Request - State: closed - Opened by pinin4fjords about 3 years ago - 1 comment

#106 - Fix mito calculations

Pull Request - State: closed - Opened by pinin4fjords about 3 years ago - 1 comment

#105 - Batch aware Scrublet

Pull Request - State: closed - Opened by pinin4fjords about 3 years ago

#104 - Always generate mito stats, even if not filtering by mito stats

Pull Request - State: closed - Opened by pinin4fjords about 3 years ago - 4 comments

#103 - Try unpinning umap-learn

Pull Request - State: closed - Opened by pinin4fjords about 3 years ago - 4 comments

#102 - Problems with Python 3.9.* - umap-learn<0.4.0 needed?

Issue - State: open - Opened by LustigePerson about 3 years ago - 3 comments

#101 - Is make_plot_function passing the color argument correctly for plot embed?

Issue - State: closed - Opened by pcm32 over 3 years ago - 2 comments

#100 - Make sure that paga without basis uses color if given

Pull Request - State: closed - Opened by pcm32 over 3 years ago - 3 comments

#99 - Unpin loompy

Pull Request - State: closed - Opened by pinin4fjords over 3 years ago - 1 comment

#98 - loompy version problem

Issue - State: closed - Opened by kaji331 over 3 years ago - 1 comment

#97 - Move to self-hosted runner

Pull Request - State: closed - Opened by pinin4fjords over 3 years ago

#96 - Store matrix variants

Pull Request - State: closed - Opened by pinin4fjords over 3 years ago - 6 comments

#95 - Allow annData output from plotting functions.

Pull Request - State: closed - Opened by pinin4fjords over 3 years ago - 3 comments

#94 - FDG and paga

Issue - State: closed - Opened by pinin4fjords over 3 years ago - 1 comment

#93 - Add first basic scrublet integration

Pull Request - State: closed - Opened by pinin4fjords over 3 years ago - 2 comments

#92 - n_genes in the var table

Issue - State: closed - Opened by ksenia007 almost 4 years ago - 1 comment

#91 - Add pushes to CI, limited to tags starting with 'v', for releasing

Pull Request - State: closed - Opened by pinin4fjords almost 4 years ago - 2 comments

#90 - Feature/ci to GitHub

Pull Request - State: closed - Opened by pinin4fjords almost 4 years ago - 2 comments

#89 - Remove CLI-level n_pcs hack and allow fallback to Scanpy's

Pull Request - State: closed - Opened by pinin4fjords almost 4 years ago - 6 comments

#88 - Hide singlet cell groups before marker detection

Pull Request - State: closed - Opened by pinin4fjords almost 4 years ago - 13 comments

#87 - 1.6.0 bugfixes

Pull Request - State: closed - Opened by pinin4fjords about 4 years ago - 2 comments

#86 - Add batch correction methods, Scanpy 1.6-specific things

Pull Request - State: closed - Opened by pinin4fjords about 4 years ago - 2 comments

#85 - scanpy-scripts-tests.sh does not exist

Issue - State: closed - Opened by mathog about 4 years ago - 2 comments

#84 - Update for Scanpy 1.5.1

Pull Request - State: closed - Opened by pinin4fjords about 4 years ago - 1 comment

#83 - Update dependencies

Pull Request - State: closed - Opened by pinin4fjords about 4 years ago - 3 comments

#82 - Add harmony integration to CLI

Issue - State: closed - Opened by pinin4fjords about 4 years ago - 1 comment

#81 - scanpy-scripts will not install, conflicting scipy version requirements

Issue - State: closed - Opened by mathog about 4 years ago - 9 comments

#80 - scanpy-scripts related warnings when scanpy is updated

Issue - State: closed - Opened by mathog over 4 years ago - 6 comments

#79 - [WIP] add batch correction

Pull Request - State: closed - Opened by racoonrocket over 4 years ago - 1 comment

#78 - Bump n_comps down to match low cell numbers

Pull Request - State: closed - Opened by pinin4fjords over 4 years ago - 1 comment

#77 - Error where n_comps > n_cells

Issue - State: closed - Opened by pinin4fjords over 4 years ago - 2 comments

#76 - Automatically reset PCs based on var size

Pull Request - State: closed - Opened by hewgreen over 4 years ago - 12 comments

#75 - Feature/fix svg defaults

Pull Request - State: closed - Opened by pinin4fjords over 4 years ago - 1 comment

#74 - Pass gene-symbols to embedding plot

Pull Request - State: closed - Opened by pinin4fjords almost 5 years ago - 1 comment

#73 - Allow filtering of boolean variables as categorical

Pull Request - State: closed - Opened by pinin4fjords almost 5 years ago - 2 comments

#72 - Always calculate basic stats before filtering

Pull Request - State: closed - Opened by nh3 almost 5 years ago - 2 comments

#71 - Feature/travis deploy

Pull Request - State: closed - Opened by pinin4fjords almost 5 years ago - 2 comments

#70 - Extend negative filtering to genes and other fixes

Pull Request - State: closed - Opened by nh3 almost 5 years ago - 2 comments

#69 - Feature/filtering tweaks

Pull Request - State: closed - Opened by pinin4fjords almost 5 years ago - 2 comments

#68 - Feature/negative filter

Pull Request - State: closed - Opened by nh3 almost 5 years ago - 2 comments

#67 - [WIP] Proposal to move certain observations generation to read step

Pull Request - State: closed - Opened by pcm32 almost 5 years ago - 12 comments

#66 - Feature/merge rgg

Pull Request - State: closed - Opened by pinin4fjords almost 5 years ago - 5 comments

#65 - Add heatmap plotting and some associated structural changes

Pull Request - State: closed - Opened by pinin4fjords almost 5 years ago - 1 comment

#64 - Feature/matrixplots

Pull Request - State: closed - Opened by pinin4fjords almost 5 years ago - 3 comments

#63 - Feature/dotplots

Pull Request - State: closed - Opened by pinin4fjords almost 5 years ago - 4 comments

#62 - Feature/stacked violins

Pull Request - State: closed - Opened by pinin4fjords almost 5 years ago - 6 comments

#61 - Make log tranform optional on normalisation

Pull Request - State: closed - Opened by pinin4fjords almost 5 years ago - 4 comments

#60 - h5py error on producing Loom file after FindMarkerGenes

Issue - State: closed - Opened by pcm32 almost 5 years ago - 4 comments

#59 - Allow specifying cell/gene prefix for all filtering attributes

Pull Request - State: closed - Opened by nh3 almost 5 years ago - 3 comments

#58 - UMAP broken

Issue - State: closed - Opened by pcm32 almost 5 years ago - 4 comments

#57 - Missing tsne multicore or not being able to load it

Issue - State: closed - Opened by pcm32 almost 5 years ago - 2 comments

#56 - Feature/loom3

Pull Request - State: closed - Opened by nh3 almost 5 years ago - 1 comment