Open Hub
Open Hub

 Settings |  Report Duplicate

1
I Use This!
Activity Not Available

Commits : Listings

Analyzed about 1 year ago. based on code collected about 1 year ago.
Jan 18, 2023 — Jan 18, 2024
Commit Message Contributor Files Modified Lines Added Lines Removed Code Location Date
Added some targets.XXXNNN.txt file as a reference for easy mimic'ing this type of file for new analysis.
Xavier de Pedro
More... about 9 years ago
typos
Xavier de Pedro
More... about 9 years ago
* Added chunks of code to generated updated paragraphs at the report, as written for study BRB279 * numGeneChanged R script, functions and calls have been renamed/refactored to use "numFeatureChanged" names and such (gene -> feature). * Fixed path and FileName to numFeatureChangedFC.R Bzr Project in sync with git 109af1c1 (from 2015-12-03) from study BRB279
(no author)
More... about 9 years ago
* Added .bzrignore in this bazaar project
Xavier de Pedro
More... about 9 years ago
* fixed path to NumGeneChanged (it currently resides under Rcode)
Xavier de Pedro
More... about 9 years ago
* refactoring of some file locations and removing former files (not needed for new scripts based on this one)
Xavier de Pedro
More... about 9 years ago
Added common default folders (with names used in the basicA.R script) and numGeneChangedFC.R as it's sourced within basicA.R
Xavier de Pedro
More... about 9 years ago
* Re-enabled sourcing PreparaDades.R file, and creating the dTables (for featAnot and topTab)
Xavier de Pedro Puente
More... about 9 years ago
* Fixed the generation of the NumGeneChanged (order of files read from disk did not match the order of the contrasts in the contrast matrix). Thanks Ferran for tips on the source of the issue.
Xavier de Pedro Puente
More... about 9 years ago
* draft code for Phase4 in the report: work in progress to edit html files through R code to fix absolute paths to be relative paths * missing still: add commands to copy js and css from the dTables through R code, not by hand as it is currently done * added links to Main docs (proposal, main report) * fixed wrong relative path for contrasts matrix (thanks Ferran!) * Added feature annotation reference in report (new section at the ResultsFiles.html) * split numGeneChanged in the report in two tables since it's two wide * renamed ID with Probe.Set.Name
Xavier de Pedro Puente
More... about 9 years ago
* A new new params added to the report, and other prepared to be reused later on (borrowed from Basic Pipe) * report file name renamed to ResultsFiles to match former name in the standard Basic Pipeline for microarrays. * added targets.all for the report to show all * added param to generate the dTable sorted by p.value by default
Xavier de Pedro Puente
More... about 9 years ago
* added dTable as iframe. Takes longer to load the single report containing everything, but once loaded, it's quite handy to browse almost everything through the browser.
Xavier de Pedro Puente
More... about 9 years ago
* removed functions of Miriam from basicA.R since they are now included in the AnalysisFunctions2Pack.R * fix wrong cel file dir * added basic code for the QC of raw and norm values. However, those chunks are commented out since they fail (R session crashes). Sections to include them in the report are kept (QC are created with a standard Basic Pipe run in the mean time) * split create.dTable from report.dTable. (since dTable takes a while to create, and more in sequential mode, and no need to re-create them each time we re-run the analysis to have the report updated with new sections, for instance, etc. * screenshots of veendiagrams and volcanoplots added at the report, besides the explicit link to their corresponding pdf's. * removed plot.ly heatmpas from the report, since they are not production ready. * show samples2remove with bold font in report * fix screenshot generation and links to png and pdf files for volcanoplots and vennDiagrams. * add the position of the link to a results file below the corresponding screenshot. * fix links to topTable dTable objects * Show file Type after the label "File:" (e.g. "File (PDF):"
Xavier de Pedro Puente
More... about 9 years ago
Collapsing the samples to remove data into one single string so that it's properly displayed at teh paragraph in Nozzle
Xavier de Pedro Puente
More... about 9 years ago
Starting point from the Rnw before any edition for BRB 279
Xavier de Pedro Puente
More... about 9 years ago
* Changed Quality control embedded results from normalized to rawdata (so that the researcher can see why some samples were removed later on) * also indicate which samples were removed from further analysis (if any), from the param used in the analysis.
Xavier de Pedro Puente
More... about 9 years ago
* eliminada la paralelització with foreach (canviada la crida de %dopar% per %do%), per tal d'evitar els problemes de que les seccions a afegir a l'informe es perdien de memoria en sortir del codi paral·lelitzat, i no he trobat en poc temps forma fàcil de recuperar-les de l'objecte retornat del bucle paral·lelitzat en acabar). * informe ja té enllaços amb ruta relativa a tots els arxius generats que s'han d'entregar a l'investigador. * deshabilitat temporalment la creació de les taules dinàmiques de topTables per a fer les re-execucions més ràpides. * corregit typo en nom d'arxiu "celsfiles.in.comparison" per "celfiles.in.comparison" * make optional de creation of plotly heatmaps, posting to plot.ly and inclusion to the report. * added a bunch of settings to the report (maintainer info, contact info, copyright info).
Xavier de Pedro Puente
More... about 9 years ago
Many changes! * paths of files are relative (for Nozzle to work as expected with file links) * Noozle report includes (in theory html sections with links to produced output files * made a dynamic way to exclude some cel files from the analysis, without requiring to edit the targets file on disk, nor the miRNA source expression data or R expression set Objects by hand, nor remove CEL files from the stored celfiles folder before running the ReadAffy() function. * Added the functions to get the feature names associated with each part of a vennDiagram: intersect, union, setdiff (thanks Miriam Mota!)
Xavier de Pedro Puente
More... about 9 years ago
Some more lines added to test the report generation, including some linked table, plus image as figure in png and linked pdf as high resolution file.
Xavier de Pedro Puente
More... about 9 years ago
Fixed topTable object being deleted from memory when run chunk in paralell; create it before parallel chunk so that it stays for later re-use in venn diagrams.
Xavier de Pedro Puente
More... about 9 years ago
Afegida la línia per a tenir en compte també la comparació cancer vs. control
Xavier de Pedro Puente
More... about 9 years ago
* code to have plot.ly create the heatmap chart online with username and api key for user ueb, plus examples of url to embed dynamic image in reports * code added to have some proof of concept of Noozle Report
Xavier de Pedro Puente
More... about 9 years ago
Added checks to the existance f objects before attempting to remove them. Added list of multiple comparison groups and the comparison names they contain each
Xavier de Pedro Puente
More... about 9 years ago
desactivat plotly /(només em va a portatil amb whir externa), i feta prova de concepte amb Nozzle.R1 per a reports
Xavier de Pedro Puente
More... about 9 years ago
Heatmaps generated and saved as pdf on disk
Xavier de Pedro Puente
More... about 9 years ago
topTables ara tenen les columnes de valors d'expressió de les mostres corresponents a la comparació en qüestió
Xavier de Pedro Puente
More... about 9 years ago
Arreglat bug de nombre d'elements erroni a listVenn per a la funció de fer el vennDiagram, i posat condicional per a que només el faci quan hi hagi 2 o més comparacions al grup.
Xavier de Pedro Puente
More... about 9 years ago
* Afegit doMC per a parallel processing a la creació dels arxius html de topTables (que triguen uns quants minuts cadascun) * Afegit codi per a la creació de les topTale in html amb columnes ordenables i filtrables a temps real amb caixa de cerca comuna. * corregit tema de hardcoding paramtres pValue i adjMethod per a numgeneschanged i toptables, però parametritzat després (VennDiagrams, etc) * pendent arreglar codi bucle creació vendiagrams, que s'atura després del primer pdf fet, en passar a la següent comparació multiple.
Xavier de Pedro Puente
More... about 9 years ago
retocs per a l'estudi BRB279. I afegit el codi R per a basicAnalysis (basicA.R)
Xavier de Pedro Puente
More... about 9 years ago
Ara si que coincideixen (as.character() was needed!) I fix per a crida a mart (assignar a objecte emprat posteriroment al codi nostre)
Xavier de Pedro Puente
More... about 9 years ago