I'm attempting to follow the supplementary analysis workflow you have kindly provided to familiarize myself with analyzing more complex data set before applying URD to my own data set. In the markdown files provided you link to two .rds files ("zf.dropseq.counts.rds" and "zf.dropseq.metadata.rds") which appear to be the unprocessed, unnormalized counts and associated metadata that are the starting point for analysis.
However these files don't appear to be on your Github repository, and the files found on the Broad SC Portal that I can see here seem to include the metadata text file but only what appears to be a fully processed object that has been run through the entire workflow (URD_Zebrafish_Object.rds). The only count file available on this repository (URD_Dropseq_Expression_Log2TPM.txt.gz) appears to already be normalized and log transformed. Are these the two files that should be used for the beginning of the analysis workflow, or is there another unnormalized count matrix that is missing from the repository? If so, would you mind updating it to include that file so that the supplementary analysis workflow can be replicated from beginning to end?
Thanks very much in advance for your help and for providing such a useful and exciting tool for us devbio nerds!
Hi there,
I'm attempting to follow the supplementary analysis workflow you have kindly provided to familiarize myself with analyzing more complex data set before applying URD to my own data set. In the markdown files provided you link to two .rds files ("zf.dropseq.counts.rds" and "zf.dropseq.metadata.rds") which appear to be the unprocessed, unnormalized counts and associated metadata that are the starting point for analysis.
However these files don't appear to be on your Github repository, and the files found on the Broad SC Portal that I can see here seem to include the metadata text file but only what appears to be a fully processed object that has been run through the entire workflow (URD_Zebrafish_Object.rds). The only count file available on this repository (URD_Dropseq_Expression_Log2TPM.txt.gz) appears to already be normalized and log transformed. Are these the two files that should be used for the beginning of the analysis workflow, or is there another unnormalized count matrix that is missing from the repository? If so, would you mind updating it to include that file so that the supplementary analysis workflow can be replicated from beginning to end?
Thanks very much in advance for your help and for providing such a useful and exciting tool for us devbio nerds!