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AlexsLemonade
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refinebio-examples
Example workflows for refine.bio data
https://www.refine.bio
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Polish the RNA-seq ORA example
#432
jaclyn-taroni
closed
3 years ago
0
Part 1: Add rownames.print = FALSE where its helpful
#431
cansavvy
closed
3 years ago
2
Polish the microarray ORA notebook
#430
jaclyn-taroni
closed
3 years ago
0
Minor Polish Diff Expr RNAseq
#429
jashapiro
closed
3 years ago
0
Remove rownames from printed tables
#428
jashapiro
closed
3 years ago
6
Changes to differential exp microarray notebook
#427
jashapiro
closed
3 years ago
3
Heatmap polish
#426
jashapiro
closed
3 years ago
0
Move filtering to before DESeq2 object creation
#425
cansavvy
closed
3 years ago
1
Update html output for RNA-seq GSEA example
#424
cbethell
closed
3 years ago
0
Umap polish
#423
jashapiro
closed
3 years ago
0
Use download.file for the three other notebooks
#422
cansavvy
closed
3 years ago
0
PCA polishing edits
#421
jashapiro
closed
3 years ago
0
PR 2 of 2: Add RNA-seq Pathway Analysis - GSEA example (take 2)
#420
cbethell
closed
3 years ago
0
PR 1 of 2: Add RNA-seq Pathway Analysis - GSEA example (take 2)
#419
cbethell
closed
3 years ago
0
Try out a different download strategy for ORA
#418
cansavvy
closed
3 years ago
0
RNA-seq examples updates: Move filtering before DESeqDataSet creation
#417
cansavvy
closed
3 years ago
0
RNA-seq DGE dataset switch
#416
cansavvy
closed
3 years ago
0
The "Getting familiar with `clusterProfiler`'s options" section of ORA examples describes `msigdbr`
#415
jaclyn-taroni
closed
3 years ago
1
Carry over common comment changes
#414
jashapiro
closed
3 years ago
1
Use same download.file strategy for ortholog RNA-seq example
#413
cansavvy
closed
3 years ago
0
For URL read in steps, change to `download.file()` for less confusion
#412
cansavvy
closed
3 years ago
0
Try different strategy for ortholog file download
#411
cansavvy
closed
3 years ago
1
Expand "Purpose of this Analysis"
#410
jashapiro
opened
3 years ago
1
Editing/polish of microarray heatmap notebook
#409
jashapiro
closed
3 years ago
4
PR 2 of 2: Add RNA-seq Pathway Analysis - GSEA example
#408
cbethell
closed
3 years ago
1
Link citations in render
#407
jashapiro
closed
3 years ago
0
Enforce code width limit
#406
jashapiro
closed
3 years ago
2
PR 1 of 2: Add RNA-seq Pathway Analysis - GSEA example
#405
cbethell
closed
3 years ago
6
GSVA for RNA-seq: Part 2 -- GSVA and a heatmap
#404
cansavvy
closed
3 years ago
0
GSVA for RNA-seq Part 1: Set up
#403
cansavvy
closed
3 years ago
0
Add rendering options
#402
jashapiro
closed
3 years ago
0
Add GSVA package to Dockerfile
#401
cbethell
closed
3 years ago
0
Add `GSVA` package to Dockerfile
#400
cbethell
closed
3 years ago
0
Control the width of output blocks
#399
jashapiro
closed
3 years ago
2
Add message = FALSE to mute chatty blocks
#398
jashapiro
closed
3 years ago
0
WIP: Add RNA-seq Pathway Analysis - GSEA Example
#397
cbethell
closed
3 years ago
23
Draft: GSVA for RNA-seq
#396
cansavvy
closed
3 years ago
5
ORA RNA-seq: Part 2 - Run ORA and get results!
#395
cansavvy
closed
3 years ago
5
ORA RNA-seq: Part 1 - The Set Up
#394
cansavvy
closed
3 years ago
1
ORA upset plot is not saved, only enrich plot 2x!
#393
cansavvy
closed
3 years ago
1
Remove getting started zip file
#392
cansavvy
closed
3 years ago
0
Publish microarray GSEA to master after intro is complete
#391
cansavvy
closed
3 years ago
0
Publish microarray GSVA to master after intro is complete
#390
cansavvy
closed
3 years ago
0
Publish internal changes (and footer)
#389
cansavvy
closed
3 years ago
1
Publish internal changes to master
#388
cansavvy
closed
3 years ago
0
Publish non squash (take 3)
#387
cansavvy
closed
3 years ago
0
Publish non squashed (take 2)
#386
cansavvy
closed
3 years ago
0
Publish other non-squashed changes
#385
cansavvy
closed
3 years ago
1
Publish WGCNA example!
#384
cansavvy
closed
3 years ago
5
Publish 3 new examples (and some other changes)
#383
cansavvy
closed
3 years ago
2
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