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Upgrade to usethis functions #42

Merged
merged 128 commits into from
Oct 31, 2024
Merged

Upgrade to usethis functions #42

merged 128 commits into from
Oct 31, 2024

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lpantano
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@lpantano lpantano commented Jul 25, 2024 •
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  • re-structure templates
  • Add text with best practices
  • Reproducibility:
    • test data for RNAseq, singlecell, CHIPseq
  • Base project:
    • Guidelines to create repo easily
    • Example Rmd with headers and aesthetics
  • RNASEQ
    • Use provenance for FA in DE report
    • Support multiple comparisons
  • New templates:
    • methylation - draft
    • singcell cell QC and Inegration - stable
    • scQC shiny app - stable
    • chipseq QC and Diffbind - beta
    • COSMX - draft

lpantano and others added 30 commits May 29, 2024 07:25
@lpantano
Initial commit
dd1b5b5
@lpantano
working code to deploy rnaseq
6b4b525
@lpantano
update DESCRIPTION
3b5300d
@lpantano
add app project name
f8ee357
@lpantano
fix typo
cc29d40
@lpantano
fixing readme and typos in DEG
271086e 
Merge branch 'devel' into magic

# Conflicts:
#	R/hello.R
@eberdan
Update DEG.Rmd
f921522 
added extra filtering
@eberdan
first part drafted
0aa7569
@eberdan
finished first draft
8e236c1
@lpantano
Merge branch 'main' into hot_fix_release
396b167
@eberdan
changed how object saved
f788824
@eberdan
initial QC
3a4ed73
@eberdan
few edits
3981525
@lpantano
org DE code, add pairwise comparison
2770e95
@lpantano
add intersection analysis
531a518
@abartlett004
cellchat template
9702600
@lpantano
Merge remote-tracking branch 'origin/cellchat' into extend_de
3087a0a
@lpantano
Merge remote-tracking branch 'origin/emma-scrna' into extend_de
c322f2d
@lpantano
move to templates
48f1b44
@lpantano
merge magic
4c723f1
@lpantano
save QC
2a4cf2f
@lpantano
small fix
7918f2c
@lpantano
Initial commit
cff4a5c
@lpantano
update readme and get working projects
304c57d
@lpantano
remove rmarkdown
9b83b1f
@lpantano
reorg singlecell
57f4545
@lpantano
move cell chat
cb64952
@lpantano
remove common information
ef4f805
@lpantano
rename integration
19efbff
@lpantano
remove base project information from analysis
fe38272
abartlett004 and others added 29 commits October 3, 2024 21:37
@abartlett004
begin feedback from meeting
c9d6339
@abartlett004
merge with remote
eda970d
@lpantano
fix rnaseq readme and add sc test dataset
98ac197
@lpantano
merge changes
d3a8047 
Merge branch 'devel' of github.com:bcbio/bcbioR into devel

# Conflicts:
#	inst/templates/rnaseq/README.md
@lpantano
adding checks and status to all rmd
1b7dc26
@lpantano
remove former hcbc readme
1dad379
@abartlett004
add venn diagram to chipseq qc
282c730
@abartlett004
merge chipseq qc
7e9001d
@abartlett004
start edits to diffbind
a0ad6c9
@abartlett004
annotation and ora for diffbind, fix typo in DEG.Rmd
1e718b3
@lpantano
fix checking version text and finish sc integration
c1aa8fc
@lpantano
fix conflict
983a73d 
Merge branch 'devel' of github.com:bcbio/bcbioR into devel

# Conflicts:
#	inst/templates/chipseq/diffbind/diffbind.Rmd
@abartlett004
QC test data working from github
12d00d3
@abartlett004
diffbind example data in github
d292490
@abartlett004
merge with remote
f32a8cf 
Merge branch 'devel' of https://github.com/bcbio/bcbioR into devel

# Conflicts:
#	inst/templates/chipseq/QC/QC.Rmd
#	inst/templates/chipseq/diffbind/diffbind.Rmd
@abartlett004
tweak cb friendly documentation, add white_to_blue palette
d96ea74
@lpantano
pass R check
ec29522
@lpantano
add rsession to sc report. Fix missing org folder.
2d2a8fd
@lpantano
add chipseq reports
1aec40d
@lpantano
error on errors only
c3879f4
@lpantano
fix chipseq test run. Add rnaseq checklist
6cdd13e
@lpantano
make names portable
d26030d
@eberdan
Add files via upload
cf8955e
@lpantano
update checklist and fix FA geneset source
cb51dbb
@lpantano
don't copy over docx source for checklist
4428530
@lpantano
adding some file names examples
fe956aa
@lpantano
fix github command to point to our org.
d244712
@lpantano
Fix naming, and better example Rmd
f6a9f5a
@lpantano
update NEWs before release
74654ec
@lpantano lpantano merged commit 3a72be5 into main Oct 31, 2024
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3 participants
@lpantano @eberdan @abartlett004