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Recent Releases of https://github.com/alexslemonade/scpca-paper-figures

https://github.com/alexslemonade/scpca-paper-figures - ScPCA paper figures v0.1.1

This is the second release of the paper figures repository, which was created in anticipation of updating the preprint on bioRxiv and submitting the manuscript to a journal.

What's Changed

  • Add columns for 10X kits to modality table by @allyhawkins in https://github.com/AlexsLemonade/scpca-paper-figures/pull/86
  • Update sample numbers in figure panels and tables by @allyhawkins in https://github.com/AlexsLemonade/scpca-paper-figures/pull/87
  • Update compiled Figure 1 with new panels by @allyhawkins in https://github.com/AlexsLemonade/scpca-paper-figures/pull/89
  • Establish deconvolution directory and sync salmon files by @sjspielman in https://github.com/AlexsLemonade/scpca-paper-figures/pull/102
  • Update figure icons to use h5ad by @allyhawkins in https://github.com/AlexsLemonade/scpca-paper-figures/pull/103
  • Add script to calculate TPM by @sjspielman in https://github.com/AlexsLemonade/scpca-paper-figures/pull/105
  • Update renv.lock and fix scripts accordingly by @sjspielman in https://github.com/AlexsLemonade/scpca-paper-figures/pull/108
  • Explore quantiseq tumor gene expression by @sjspielman in https://github.com/AlexsLemonade/scpca-paper-figures/pull/109
  • Add script to run quanTIseq by @sjspielman in https://github.com/AlexsLemonade/scpca-paper-figures/pull/110
  • Regenerate manuscript figures by @sjspielman in https://github.com/AlexsLemonade/scpca-paper-figures/pull/113
  • Add exploratory quantiseq results notebook by @sjspielman in https://github.com/AlexsLemonade/scpca-paper-figures/pull/112
  • Update sample numbers for Figure 1 and supplemental tables by @allyhawkins in https://github.com/AlexsLemonade/scpca-paper-figures/pull/106
  • Recompile figures, PR 1/~3 by @sjspielman in https://github.com/AlexsLemonade/scpca-paper-figures/pull/115
  • Add script for EPIC deconvolution by @sjspielman in https://github.com/AlexsLemonade/scpca-paper-figures/pull/118
  • Update images in Figure 3 and recompile by @allyhawkins in https://github.com/AlexsLemonade/scpca-paper-figures/pull/121
  • Update compilations for S4-S7 by @sjspielman in https://github.com/AlexsLemonade/scpca-paper-figures/pull/119
  • Notebook to explore EPIC results by @sjspielman in https://github.com/AlexsLemonade/scpca-paper-figures/pull/120
  • Recompile Figure 1 by @allyhawkins in https://github.com/AlexsLemonade/scpca-paper-figures/pull/123
  • Add epic/quantiseq comparison notebook by @sjspielman in https://github.com/AlexsLemonade/scpca-paper-figures/pull/122
  • Set up pseudobulk analysis and TPM data by @sjspielman in https://github.com/AlexsLemonade/scpca-paper-figures/pull/133
  • Calculate and compare pseudobulk measures by @sjspielman in https://github.com/AlexsLemonade/scpca-paper-figures/pull/134
  • Modify notebook name by @sjspielman in https://github.com/AlexsLemonade/scpca-paper-figures/pull/137
  • Notebook to build and compare linear models by @sjspielman in https://github.com/AlexsLemonade/scpca-paper-figures/pull/139
  • Modify model notebook parsing and export by @sjspielman in https://github.com/AlexsLemonade/scpca-paper-figures/pull/141
  • Export tables of gene expression percentage across samples by @sjspielman in https://github.com/AlexsLemonade/scpca-paper-figures/pull/145
  • Update model notebook with filter parameter by @sjspielman in https://github.com/AlexsLemonade/scpca-paper-figures/pull/149
  • Explore residual distributions across annotation status by @sjspielman in https://github.com/AlexsLemonade/scpca-paper-figures/pull/150
  • Notebook to run GSEA with shuffled gene sets by @sjspielman in https://github.com/AlexsLemonade/scpca-paper-figures/pull/151
  • Establish ESTIMATE analysis directory by @sjspielman in https://github.com/AlexsLemonade/scpca-paper-figures/pull/156
  • Add script to prepare data for estimate by @sjspielman in https://github.com/AlexsLemonade/scpca-paper-figures/pull/157
  • Notebook to run estimate by @sjspielman in https://github.com/AlexsLemonade/scpca-paper-figures/pull/158
  • Notebook to compare ESTIMATE to consensus cell types by @sjspielman in https://github.com/AlexsLemonade/scpca-paper-figures/pull/160
  • Add considerations for low-quality cells by @sjspielman in https://github.com/AlexsLemonade/scpca-paper-figures/pull/163
  • Revive scatterplots with bulk ESTIMATE scores by @sjspielman in https://github.com/AlexsLemonade/scpca-paper-figures/pull/170
  • Add missing sample to analysis by @sjspielman in https://github.com/AlexsLemonade/scpca-paper-figures/pull/173
  • Create geneset TSVs for ORA by @sjspielman in https://github.com/AlexsLemonade/scpca-paper-figures/pull/171
  • Add notebook and results for ORA by @sjspielman in https://github.com/AlexsLemonade/scpca-paper-figures/pull/175
  • Add odds ratio summary notebook by @sjspielman in https://github.com/AlexsLemonade/scpca-paper-figures/pull/177
  • Add script to sync consensus celltype results by @allyhawkins in https://github.com/AlexsLemonade/scpca-paper-figures/pull/185
  • Remove Fig S6 and S7 by @allyhawkins in https://github.com/AlexsLemonade/scpca-paper-figures/pull/192
  • Try duckplyr for memory efficiency by @jashapiro in https://github.com/AlexsLemonade/scpca-paper-figures/pull/194
  • Export model data as separate TSV by @sjspielman in https://github.com/AlexsLemonade/scpca-paper-figures/pull/196
  • Create all the dot plots for Fig 5A and S6 by @allyhawkins in https://github.com/AlexsLemonade/scpca-paper-figures/pull/193
  • Update the gene set script by @sjspielman in https://github.com/AlexsLemonade/scpca-paper-figures/pull/197
  • Update the overrepresentation analysis and results by @sjspielman in https://github.com/AlexsLemonade/scpca-paper-figures/pull/198
  • Update GSEA notebooks by @sjspielman in https://github.com/AlexsLemonade/scpca-paper-figures/pull/199
  • Update README and other analysis housekeeping by @sjspielman in https://github.com/AlexsLemonade/scpca-paper-figures/pull/205
  • Update dotplot widths by @sjspielman in https://github.com/AlexsLemonade/scpca-paper-figures/pull/207
  • Get rid of tpm lines by @sjspielman in https://github.com/AlexsLemonade/scpca-paper-figures/pull/213
  • Add Figure S6 compilation by @sjspielman in https://github.com/AlexsLemonade/scpca-paper-figures/pull/210
  • Add table with bulk analysis manuscript numbers by @sjspielman in https://github.com/AlexsLemonade/scpca-paper-figures/pull/202
  • Add code and PDFs for bulk figures by @sjspielman in https://github.com/AlexsLemonade/scpca-paper-figures/pull/203
  • Add bar chart for HGG vs. LGG showing all celltypes by @allyhawkins in https://github.com/AlexsLemonade/scpca-paper-figures/pull/208
  • Supplemental figure 7 barplots for remaining diagnosis groups by @allyhawkins in https://github.com/AlexsLemonade/scpca-paper-figures/pull/218
  • Use SCPCL000498 for both panels in S5 by @allyhawkins in https://github.com/AlexsLemonade/scpca-paper-figures/pull/222
  • Add celltype project file to sample-info by @sjspielman in https://github.com/AlexsLemonade/scpca-paper-figures/pull/230
  • Add standalone sample whitelist and script to generate it by @sjspielman in https://github.com/AlexsLemonade/scpca-paper-figures/pull/215
  • Add compiled bulk figures: 6 and S8 by @sjspielman in https://github.com/AlexsLemonade/scpca-paper-figures/pull/232
  • Compile S7 and update fonts in S6 by @allyhawkins in https://github.com/AlexsLemonade/scpca-paper-figures/pull/226
  • Add bar chart for HGG vs. LGG highlighting immune celltypes by @sjspielman in https://github.com/AlexsLemonade/scpca-paper-figures/pull/209
  • Add compiled figure 5 by @sjspielman in https://github.com/AlexsLemonade/scpca-paper-figures/pull/238
  • Review first: Establish reproducibility directory by @sjspielman in https://github.com/AlexsLemonade/scpca-paper-figures/pull/237
  • Export S1B-D benchmarking data TSVs by @sjspielman in https://github.com/AlexsLemonade/scpca-paper-figures/pull/225
  • Update repo and script READMEs by @sjspielman in https://github.com/AlexsLemonade/scpca-paper-figures/pull/235
  • Add metadata script by @sjspielman in https://github.com/AlexsLemonade/scpca-paper-figures/pull/246
  • Document ORA tsvs by @sjspielman in https://github.com/AlexsLemonade/scpca-paper-figures/pull/248
  • Filter to only samples used in analysis by @sjspielman in https://github.com/AlexsLemonade/scpca-paper-figures/pull/249
  • Add script to prepare all the scpca data by @sjspielman in https://github.com/AlexsLemonade/scpca-paper-figures/pull/251
  • Consolidate into a single reproducibility script by @sjspielman in https://github.com/AlexsLemonade/scpca-paper-figures/pull/256
  • Sync the panglao references by @sjspielman in https://github.com/AlexsLemonade/scpca-paper-figures/pull/257
  • Account for SCEs without consensus cell types by @sjspielman in https://github.com/AlexsLemonade/scpca-paper-figures/pull/258
  • Update metadata parsing by @sjspielman in https://github.com/AlexsLemonade/scpca-paper-figures/pull/261
  • Reproducibility testing miscellany by @sjspielman in https://github.com/AlexsLemonade/scpca-paper-figures/pull/266
  • Analysis reproducibility fixes by @sjspielman in https://github.com/AlexsLemonade/scpca-paper-figures/pull/268
  • Redux of #268 by @sjspielman in https://github.com/AlexsLemonade/scpca-paper-figures/pull/270
  • Update compiled Figures 1 and S5 by @sjspielman in https://github.com/AlexsLemonade/scpca-paper-figures/pull/269
  • Update panel 3D and code by @sjspielman in https://github.com/AlexsLemonade/scpca-paper-figures/pull/273
  • Update compiled figure 3 by @sjspielman in https://github.com/AlexsLemonade/scpca-paper-figures/pull/274
  • Add reproducibility instructions by @sjspielman in https://github.com/AlexsLemonade/scpca-paper-figures/pull/271
  • Update Figure S7 sizing by @sjspielman in https://github.com/AlexsLemonade/scpca-paper-figures/pull/275
  • Fix sample numbers for modality bar chart Fig 1B by @allyhawkins in https://github.com/AlexsLemonade/scpca-paper-figures/pull/277
  • Align Fig 6 & S8 legends by @sjspielman in https://github.com/AlexsLemonade/scpca-paper-figures/pull/281
  • Reproducibility updates for consensus cell types by @sjspielman in https://github.com/AlexsLemonade/scpca-paper-figures/pull/282

New Contributors

  • @jashapiro made their first contribution in https://github.com/AlexsLemonade/scpca-paper-figures/pull/194

Full Changelog: https://github.com/AlexsLemonade/scpca-paper-figures/compare/v0.1.0...v0.1.1

- HTML
Published by jaclyn-taroni about 1 year ago

https://github.com/alexslemonade/scpca-paper-figures - ScPCA paper figures v0.1.0

What's Changed

This is the first release of the figures used in the ScPCA manuscript. The manuscript is located in AlexsLemonade/ScPCA-manuscript.

New Contributors

  • @allyhawkins made their first contribution in https://github.com/AlexsLemonade/scpca-paper-figures/pull/12
  • @sjspielman made their first contribution in https://github.com/AlexsLemonade/scpca-paper-figures/pull/32
  • @dvenprasad made their first contribution in https://github.com/AlexsLemonade/scpca-paper-figures/pull/50
  • @jaclyn-taroni made their first contribution in https://github.com/AlexsLemonade/scpca-paper-figures/pull/85

Full Changelog: https://github.com/AlexsLemonade/scpca-paper-figures/commits/v0.1.0

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Published by allyhawkins over 2 years ago