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

New Contributors

• @jashapiro made their first contribution in #194

Full Changelog: v0.1.0...v0.1.1