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ByrumLab
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proteoDA
GNU General Public License v3.0
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Limma report file checks 196
#204
tjthurman
closed
1 year ago
0
S3 class checks
#203
tjthurman
closed
1 year ago
0
rename vignettes folder and add paper folder to RBuildIgnore
#202
tjthurman
closed
1 year ago
0
Vigenette: render as a pdf
#201
ByrumLab
closed
1 year ago
5
Vignette: add the two png images in vignette/images to the Rmd and describe output
#200
ByrumLab
closed
1 year ago
1
add vignette example
#199
sbyrum21
closed
1 year ago
0
For add_design and add_contrasts, overwrite downstream things if they're already present
#198
tjthurman
closed
1 year ago
0
DOC: minor edits to documentation
#197
sbyrum21
closed
1 year ago
0
Final file checks in write_limma_report
#196
tjthurman
closed
1 year ago
0
Add paper.md and references.bib to a paper directory
#195
sbyrum21
closed
1 year ago
0
Move read_DIA_data and add_metadata to internal R package
#194
tjthurman
closed
1 year ago
0
remove UAMS fxn filter_proteins_contaminants
#193
tjthurman
closed
1 year ago
0
Report cols 123
#192
tjthurman
closed
1 year ago
0
Vignette example workflow and data
#191
sbyrum21
closed
1 year ago
1
Default output dir 188
#190
tjthurman
closed
1 year ago
0
S3 class checks
#189
tjthurman
closed
1 year ago
0
change output directory defaults for all writing functions
#188
tjthurman
closed
1 year ago
1
Test limma analysis
#187
tjthurman
closed
1 year ago
0
removing extra files
#186
tjthurman
closed
1 year ago
0
improve description for CRAN
#185
tjthurman
closed
1 year ago
0
Update Rbuildignore to reflect new package name
#184
tjthurman
closed
1 year ago
0
rename from _DE_report to _DA_report
#183
tjthurman
closed
1 year ago
0
Some more package renaming in report template files
#182
tjthurman
closed
1 year ago
0
rename the package
#181
tjthurman
closed
1 year ago
0
Typos in documentation
#180
dhalkam
closed
1 year ago
0
Test add contrasts
#179
tjthurman
closed
1 year ago
0
Rename public package and repo
#178
tjthurman
closed
1 year ago
1
write_norm_report now saves normQCmetrics as in the tags
#177
jbird9
closed
1 year ago
3
Update package to use the S3 object
#176
tjthurman
closed
1 year ago
0
administrative changes before S3 merge
#175
tjthurman
closed
1 year ago
0
Require uniprot_id column in annotation
#174
tjthurman
closed
1 year ago
1
Deprecate or remove filter_protein_contaminants
#173
tjthurman
closed
1 year ago
2
Uniprot required column
#172
tjthurman
closed
1 year ago
1
add per-group dots into the normalization report output
#171
tjthurman
closed
1 year ago
0
proteiNorm plots should show the dots for each sample group
#168
ByrumLab
closed
1 year ago
4
tests for normalization functions
#167
tjthurman
closed
1 year ago
0
add tests for add_design
#166
tjthurman
closed
1 year ago
0
Protein filter tests
#165
tjthurman
closed
1 year ago
0
NA handling
#164
tjthurman
closed
1 year ago
0
Filter fxn tests
#163
tjthurman
closed
1 year ago
0
External constructor
#162
tjthurman
closed
1 year ago
0
convert missing data to NA in read_DIA_data
#161
tjthurman
closed
1 year ago
0
Don't convert 0 values to NA in filtering functions
#160
tjthurman
closed
1 year ago
1
Helper functions to convert 0 to NA and vice-versa in data section of DAList
#159
tjthurman
closed
1 year ago
1
Convert missing values to NA, not 0, when importing data with read_DIA_data
#158
tjthurman
closed
1 year ago
0
Rename DIAlist to DAList
#157
tjthurman
closed
1 year ago
0
Remove ilab argument from write_limma_tables
#156
tjthurman
closed
1 year ago
0
Change the rownames back to UniprotIDs and not "protein123".
#155
sbyrum21
closed
1 year ago
1
Filter samples test and doc
#154
tjthurman
closed
1 year ago
0
add_metadata documentation
#153
sbyrum21
closed
1 year ago
0
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