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Workflow separations & Correlation Analysis #48

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Workflow separations & Correlation Analysis #48

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Workflow Separation

  • Created three different workflows: Microbial, Host Expression, and Integrative Analysis.
  • Microbial is the same as 'animalcules' before any changes, and Integrative Analysis includes the Correlations tab. Host Expression still needs some more functionality to be filled out
  • Workflows will only pop up if the corresponding assay is present

Correlation Analysis

  • Users can select two assays to correlate against one another. Subsequently, can do Co-Occurence Network and Enrichment analyses

Also updated vignettes to include instructions for usage.

Saket Pandit added 30 commits March 27, 2021 19:42
Correlation shiny UI
6e728db
Correlations shiny server
85c3535
Correlations R functions
0058cec
Adding 'updateAssays' session function to keep track of assays in MAE
cbd17b5
Man files for these functions
f0a4fd1
Man file for rd_MAE
80d70a4
slight change to corr_func, changed name
de1b1ff
updated to also include correlations
a74b625
Added mae.assays
06d6edd
Updated to include Workflow tabs + Correlations
de27a01
Fixed a typo
55d6506
Fixed another typo
ddb2e94
manual for genes_gsva_dimred.R function
59a81b1
Function for GSVA analysis / dimension reduction
e377c9d
Including genes_dimred_gsva
34bbb20
Adding in a GSVA tab
1bba342
Server function for GSVA tab
14b069f
UI function for GSVA tab
da8d479
Adding in MSigDB collections, used in GSVA tab
814a487
Now includes genes_dimred_gsva.R
9b700c6
Commented out tags$style(appCSS)
e43ff71
Modified so that the function now creates the plot + summary table. N…
a4cc179 
…o longer relying on shiny app to do so
Fixed some small typos, made calc_sig *slightly* faster
58f74bb
Modified corr_func so that it will also produce a plot, summary, and …
b519c41 
…top 10 summary table
Modified shiny scripts so that none of the "correlations" section is …
4d71c06 
…done on shiny. Also, integrated enrichment with hypeR
added hypeR library
ac5e8aa
Changed so that enrichment is also not done on Rshiny
c8c674c
No longer need to connect to enrichR, using hypeR
45f47d3
Including updated corr_func and enrich_cors
cf27095
Now includes summary_cors, heatmap_cors, and enrich_cors
8e17f7a
Saket Pandit added 30 commits June 23, 2021 20:57
Fixed so that it will work even if Group_Size = 1
87baf50
Fixed issue where not all groups were displaying, only positive corre…
d230331 
…lations would show up
Added in interactive summary table for the split conditions (main pag…
2bbd8b6 
…e + co-occurence network)
Forgot to add "@export" for the function
bd70ee6
Added "@export", and also sort the rows_selected parameter before doi…
cfb1443 
…ng anything with it
Changed to match the new column names produced by summary_cors (Group…
42a90b6 
…, Correlates)
Added interactive enrichment table
dce8d80
Better documentation
306aff6
Added descriptive text for clearer instructions
d3945ff
commented out loading R library (testing)
37081ab
Commented out GO_Biological_Process (temp)
3447fc4
Added more descriptive text, specifically for split conditions
a3bda8b
Only allowing single row selection for co-occurence networks + enrich…
6bf7aa4 
…ment tables
Created a separate function to insert the ssGSEA scores into the Mult…
e6f7ed6 
…iAssayExperiment. Also, fixed a problem where new ssGSEA scores would not insert
Fixed example
a7caa5d
Changed gene names from Ensembl ID to Gene Symbol
e6b6fea
Integrates use of insert_into_MAE() and path_proj()
09ee2dd
Cleaned up code (clearer commenting/documentation)
2402a45
Fixed issue with reading in assays and displaying the correct Tabs / …
45b0dd7 
…Workflows
Cleaned up code, comments and documentation
9782eb5
Includes insert_into_MAE()
9ba37ac
Small changes to be compliant with Bioconductor checks
0c080a7
Aesthetic changes to the example
ae85bd1
Updated to include instructions and examples for co-occurence network…
df32a6c 
…s and enrichment
Fixed issue with deprecation
8f22030
Got rid of the devtools() line, ready for final pull request
9c944fc
Removed a browser() command used during debugging
05eb01a
Removed another browser() command
a27c7ec
Fixed a problem with corr_func, is now able to handle NA values in th…
fc3bb1d 
…e assays
Fixed issue where gsva data did not insert into MAE
fe1cfa3
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