markrobinsonuzh/conquer

consistent quantification of external RNA-seq data sets

conquer's Issues

Conquer Database Website is Not Working

Hi,

I was trying to look at Conquer Database Website http://imlspenticton.uzh.ch:3838/conquer/
but the site is not working. Could you fix the problem?

Cell labels in 'characteristics_ch' of colData

If the cell labels were changed in later publications, are they get updated in these colData slots ?

Running scater_template.Rmd

> knit('scater_template.Rmd')


processing file: scater_template.Rmd
  |..                                                               |   3%
   inline R code fragments

Quitting from lines 2-6 (scater_template.Rmd) 
Error in vapply(x, format_sci_one, character(1L), ..., USE.NAMES = FALSE) : 
  values must be length 1,
 but FUN(X[[3]]) result is length 13

Also

~/Dropbox/Private/Pfizer/conquer $ R -e "rmarkdown::render('scater_template.Rmd')"

R version 3.3.2 (2016-10-31) -- "Sincere Pumpkin Patch"
Copyright (C) 2016 The R Foundation for Statistical Computing
Platform: x86_64-apple-darwin15.6.0 (64-bit)

R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.

  Natural language support but running in an English locale

R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.

Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.

> rmarkdown::render('scater_template.Rmd')


processing file: scater_template.Rmd
  |..                                                               |   3%
   inline R code fragments

Quitting from lines 2-6 (scater_template.Rmd) 
Error in eval(expr, envir, enclos) : object 'id' not found
Calls: <Anonymous> ... in_dir -> inline_exec -> withVisible -> eval -> eval

Execution halted

If I try running the R inside the .Rmd then I get errors like

> maex
Error: object 'maex' not found

Batch IDs & sample-level QC measures

Where can I find 'batch IDs' & sample-level QC measures like 'run IDs' other than the 'num_processed', 'num_mapped', & 'percent_mapped' in metadata$salmon_summary?

Adding a license?

This is great work! Would you mind adding a license to this repository so it is clear whether / how the code can be reused? Thanks in advance!