pancancer
pancancer copied to clipboard
greenelab
Building classifiers using cancer transcriptomes across 33 different cancer-types
hi, I was analyzing Ras_cell_line_predictions, the following file: mutation__gene_x_ccle_cellline.gct is missing from the data. checked the same in onco-gps-paper-analysis data folder [https://github.com/UCSD-CCAL/onco_gps_paper_analysis/tree/master/data], but could not find it. I have also...
The CCLE analysis [notebook](https://github.com/greenelab/pancancer/blob/master/scripts/ras_cell_line_predictions.ipynb) includes data without clear instructions on data access. I will need to update to make the data access instructions more clear. In the interim, the data...
Hi, I encountered some issues while running step4 of tp53 pipeline. It responds like this: Error in optparse::parse_args(opt_parser) : Error in getopt(spec = spec, opt = args) : flag "pancan_summary"...
Hi there, I am a bit confused on why you zero-one normalized the count matrix before going through the limma pipeline, so could you please give some explanations? Thanks!
As mentioned by @blankenberg in #98 > An upgrade to pandas 0.24.0+ will give 'infer' option for compression in to_csv() which is now currently being worked around for gzip outputs....
@ypar noted in #86 > it would be nicer to see some summary texts accompanying them. in their current form, they are very difficult to follow. maybe show one or...
@ypar noted in #86 > _gene_phenocopy plots are missing x axis labels? I need to update this in the future
The embargo on the data has lifted (see #75) and the paper has been published (See [`release v2.2`](https://github.com/greenelab/pancancer/releases/tag/v2.2)). Therefore, it is time to update the repo. I will use this...