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Create function: filter_counts #38

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merged 81 commits into from
Oct 8, 2024
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d9f25cf
test: write basic test for nidap filter_low_counts template
kelly-sovacool Jun 18, 2024
544ef12
refactor: break out filtering code into functions
kelly-sovacool Jun 20, 2024
adce7ec
chore: add imports for filter_counts
kelly-sovacool Jul 9, 2024
d52739a
chore: update CITATION.cff
github-actions[bot] Jul 9, 2024
52c3d80
refactor: use S7 object in filter_counts
kelly-sovacool Jul 9, 2024
8caf3d5
chore: Merge branch 'iss-35' of https://github.com/CCBR/reneeTools in…
kelly-sovacool Jul 15, 2024
b14c11b
fix: S7 validator syntax
kelly-sovacool Jul 15, 2024
8e6679f
fix: need double square brackets for named list element
kelly-sovacool Jul 15, 2024
16db85d
test: write tests for remove_low_count_genes()
kelly-sovacool Jul 15, 2024
5079bac
fix: set seed outside get_random_colors
kelly-sovacool Jul 15, 2024
9292c8b
fix: throw error when num_colors < 1
kelly-sovacool Jul 15, 2024
22ac2d1
docs: note color blind palette option
kelly-sovacool Jul 16, 2024
de115c2
refactor: remove old filter_low_counts()
kelly-sovacool Jul 17, 2024
497b5c8
fix: use pkg::fcn syntax
kelly-sovacool Jul 17, 2024
fc7c9de
test: write basic tests for validate_sample_metadata()
kelly-sovacool Jul 17, 2024
88f43e3
chore: update CITATION.cff
github-actions[bot] Jul 17, 2024
dfb9ec5
test: basic null tests for rename_samples()
kelly-sovacool Jul 23, 2024
24a209c
test: basic unit tests for plot_pca()
kelly-sovacool Jul 24, 2024
14a8751
chore: update CITATION.cff
github-actions[bot] Jul 24, 2024
7ecdf46
docs: document df param
kelly-sovacool Jul 29, 2024
8ec2ea6
refactor: rename to plot_heatmap()
kelly-sovacool Jul 29, 2024
3e4ff1f
refactor: improve plot_heatmap param names
kelly-sovacool Jul 30, 2024
b1729ab
fix: get_our_random_colors() renamed
kelly-sovacool Jul 31, 2024
cd6ced7
test: write basic tests for plot_heatmap()
kelly-sovacool Jul 31, 2024
db29180
test: add basic test for plot_histogram()
kelly-sovacool Jul 31, 2024
1789b4f
test: fix usage of reneeDS class
kelly-sovacool Jul 31, 2024
e4e69a3
refactor: set default user params as function args
kelly-sovacool Jul 31, 2024
fd4a36a
fix: warnings during testing
kelly-sovacool Jul 31, 2024
2f2f42d
fix: remove library() statements
kelly-sovacool Jul 31, 2024
c9fb525
test: write test for counts_dat_to_matrix()
kelly-sovacool Jul 31, 2024
9c4cf14
test: update deseq tests for new renee class structure
kelly-sovacool Jul 31, 2024
effee04
fix: use pkg::fcn() syntax
kelly-sovacool Jul 31, 2024
5a0e5d4
test: suppressMessages() for cleaner testthat output
kelly-sovacool Jul 31, 2024
1662643
fix: handle when filtered counts doesn't exist for deseq2
kelly-sovacool Jul 31, 2024
3a0120e
fix: most R CMD Check errors/warnings/notes
kelly-sovacool Jul 31, 2024
f30cacb
chore: update CITATION.cff
github-actions[bot] Jul 31, 2024
636acd7
Merge branch 'main' into iss-35
kelly-sovacool Aug 8, 2024
79e612e
chore: update CITATION.cff
github-actions[bot] Aug 8, 2024
c4f02f5
feat: create calc_cpm()
kelly-sovacool Aug 20, 2024
46f083e
chore: todo notes
kelly-sovacool Aug 20, 2024
38f70f5
feat: start vignette for RAM demo
kelly-sovacool Aug 20, 2024
db8fde1
feat: combine gene_id and GeneName from RENEE data
kelly-sovacool Aug 20, 2024
3b96ed7
feat: calc cpm
kelly-sovacool Aug 20, 2024
f6819d9
feat: use gene_colname variable
kelly-sovacool Aug 20, 2024
57c74bd
fix: cpm before filter [WIP]
kelly-sovacool Aug 20, 2024
020620f
test: fix all.equal comparison
kelly-sovacool Aug 20, 2024
6183267
chore: Merge branch 'filt-working-tests' into iss-35
kelly-sovacool Aug 27, 2024
09f4fd6
fix: dplyr::relocate()
kelly-sovacool Aug 27, 2024
d784555
style: separate code chunks
kelly-sovacool Aug 27, 2024
f409682
chore: update CITATION.cff
github-actions[bot] Aug 27, 2024
b1daaf9
fix: handling of combined gene_id and GeneName cols
kelly-sovacool Aug 27, 2024
e468c87
test: fix typo
kelly-sovacool Aug 27, 2024
1304acb
fix: typo
kelly-sovacool Aug 27, 2024
052cc9f
chore: build vignettes
kelly-sovacool Aug 27, 2024
4563bee
refactor: singular arg names
kelly-sovacool Aug 27, 2024
d68ef86
feat: plot memory usage vs n samples
kelly-sovacool Aug 27, 2024
0252045
chore: Merge branch 'iss-35' of https://github.com/CCBR/reneeTools in…
kelly-sovacool Aug 27, 2024
7773ad0
docs: demo S7 vs seurat memory usage
kelly-sovacool Sep 9, 2024
ce23664
fix: filter reproduces nidap results
kelly-sovacool Oct 1, 2024
d0b97c4
fix: round decimals for deseq
kelly-sovacool Oct 1, 2024
0da67de
test: fix gene names
kelly-sovacool Oct 1, 2024
64597d9
fix: don't run example for internal function
kelly-sovacool Oct 1, 2024
10bae60
style: lowercase function arguments
kelly-sovacool Oct 3, 2024
9df94f0
docs: document all params
kelly-sovacool Oct 8, 2024
2d96a92
chore: update CITATION.cff
github-actions[bot] Oct 8, 2024
c4176d1
chore: update NEWS.md
kelly-sovacool Oct 8, 2024
1f5adec
chore: Merge branch 'iss-35' of https://github.com/CCBR/reneeTools in…
kelly-sovacool Oct 8, 2024
7af5758
docs: allow memory vignette to be built
kelly-sovacool Oct 8, 2024
9f8fae6
refactor: gzip data files
kelly-sovacool Oct 8, 2024
4960852
docs: document()
kelly-sovacool Oct 8, 2024
b602d72
docs: simplify memory vignette
kelly-sovacool Oct 8, 2024
cbc06be
fix: add pkgs for memory vignette
kelly-sovacool Oct 8, 2024
8d2caf6
chore: update CITATION.cff
github-actions[bot] Oct 8, 2024
25cb0ff
fix: suppress vignette title warning
kelly-sovacool Oct 8, 2024
425469e
chore: Merge branch 'iss-35' of https://github.com/CCBR/reneeTools in…
kelly-sovacool Oct 8, 2024
6434e78
fix: filter_counts() currently requires data frames
kelly-sovacool Oct 8, 2024
eca42f5
test: filter_counts() with RENEE RSEM counts
kelly-sovacool Oct 8, 2024
646fb01
docs: demo filter_counts() in intro vignette
kelly-sovacool Oct 8, 2024
9d523ee
chore: add scales pkg for vignettes
kelly-sovacool Oct 8, 2024
f1e90ec
docs: document()
kelly-sovacool Oct 8, 2024
6707036
chore: update CITATION.cff
github-actions[bot] Oct 8, 2024
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2 changes: 2 additions & 0 deletions .Rbuildignore
Original file line number Diff line number Diff line change
Expand Up @@ -12,3 +12,5 @@
^data-raw$
^Dockerfile$
^CITATION\.cff$
^doc$
^Meta$
2 changes: 2 additions & 0 deletions .gitignore
Original file line number Diff line number Diff line change
Expand Up @@ -6,3 +6,5 @@
.quarto
docs
inst/doc
/doc/
/Meta/
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