Releases: MoTrPAC/MotrpacRatTraining6mo
Releases · MoTrPAC/MotrpacRatTraining6mo
Try try again
Summary
- In
plot_feature_normalized_data()
andplot_feature_logfc()
, handle input features that don't exist in the data.
What's Changed
Full Changelog: v1.4.2...v1.4.3
Happy plotting
Summary
- Dodge points in
plot_feature_normalized_data()
andplot_feature_logfc()
for readability. - Make
plot_feature_normalized_data()
andplot_feature_logfc()
more accommodating of features with multiple measurements. - Add
add_adj_p
parameter toplot_feature_normalized_data()
. - Add
return_data
parameter toplot_feature_logfc()
. - Return NULL instead of error if data doesn't exist for plotting
plot_feature_normalized_data()
in loops.
What's Changed
Full Changelog: v1.4.1...v1.4.2
Ladybug
Summary
- Fix
custom_cluster_pathway_enrichment()
to accept a list of lists as input. - Use filtered feature-to-gene map to perform pathway enrichment.
- In
cluster_pathway_enrichment()
, remove pathway enrichments driven by a single gene
for consistency with the landscape paper.
What's Changed
Full Changelog: v1.4.0...v1.4.1
Party gene
Summary
- Add
gene_pathway_enrichment()
(wrapper forgprofiler2::gost()
). - Add example to "Get Started" vignette.
What's Changed
Full Changelog: v1.3.0...v1.4.0
Workshop ready
Summary
- Add
df_to_numeric()
to easily format data frames. - Add
plot_feature_normalized_data()
to plot normalized sample-level data for a single feature. - Add
plot_feature_logfc()
to plot differential analysis results for a single feature. - Add more examples and screenshots to the "Get Started" vignette.
What's Changed
Full Changelog: v1.2.0...v1.3.0
Tis the season
Summary
- Add functions to perform meta-analysis and meta-regression of redundant metabolites.
- Add
load_training_da()
to load training summary statistics from GSC. - Retain order of input vial labels in result of
viallabel_to_pid()
.
What's Changed
- fix tree plot bug and speed up feature traj by @nicolerg in #33
- meta-reg and training-da by @nicolerg in #34
Full Changelog: v1.1.0...v1.2.0
Attack outliers
Summary
- Add
atac_call_outliers()
- Bug fix in
atac_prep_data()
What's Changed
Full Changelog: v1.0.2...v1.1.0
Zoomies
Summary
- Use a hashmap to speed up calculation of similarity scores in
enrichment_network_viz()
(thanks, Jay Yu) - Improve
visInteraction
settings inenrichment_network_viz()
, i.e., show edges on zoom and slow down zoom - Don't run memory-intensive examples and vignette code blocks to prevent GitHub Actions OOM error
What's Changed
Full Changelog: v1.0.1...v1.0.2
I spoke too soon
Summary
Fix bugs:
- missing
:
intranscript_timewise_da()
- counts improperly filtered in
transcript_prep_data()
DESeq2
prefix missing fromcounts()
intranscript_timewise_da()
Dev:
- keep examples from printing too much output
- rename
tutorial.Rmd
toMotrpacRatTraining6mo
to take advantage of "Get Started"pkgdown
feature - add
@keywords internal
to functions that are not exported to prevent them from showing up in site index
What's Changed
Full Changelog: v1.0.0...v1.0.1
Let's get some traffic!
Summary
- First release
- New site: https://motrpac.github.io/MotrpacRatTraining6mo/
- New vignette: https://motrpac.github.io/MotrpacRatTraining6mo/articles/tutorial.html
- Ready for submission!
What's Changed
- add load_dropbox_rdata by @nicolerg in #1
- Create proteomics_differential_analysis.R by @pierremj in #2
- RNA-seq DEA fx by @nicolerg in #3
- Add rrbs by @david-dd-amar in #4
- Add repfdr by @david-dd-amar in #5
- Major additions by @nicolerg in #13
- remove prot outliers by @nicolerg in #15
- immuno da fx by @nicolerg in #16
- Add metabolomics differential analysis by @pierremj in #14
- more fx and fewer dependencies by @nicolerg in #18
- graph pw by @nicolerg in #19
- last batch of fx by @nicolerg in #20
- add vignette by @nicolerg in #21
- add pkgdown site by @nicolerg in #22
- update links by @nicolerg in #23
Full Changelog: https://github.com/MoTrPAC/MotrpacRatTraining6mo/commits/v1.0.0