Update to input file location

1.3.1

Update singlecellproteogenomics.smk with new input file location (#11)

Optimized for cluster runs

• Allows it to be run by slurm more easily.
• Improved memory issues in making RSEM dataframes

Add options for quicker runs of protein and rna code

1.2.1

update to new scp version (#8)

Allow for discrepancies between GTF and GFFs in v103

• Uses the GTF file for the counts dataframe, as is used for RSEM
• Added information regarding running on clusters

Download and use SRAs; add SingleCellProteogenomics to pipeline

Update pipeline to download and use SRAs from GEO (#1)

* rework from sra-download

* linting

* through sras and trimming

* through making rsem-star reference

* adding velocity calculations

* working through making a_obs

* copying new results

* finish pipeline through making dataframes

* comment out testing

* update input link

* add kinase results to all to prompt full run

Original release

This is the version of the code used in the paper "Spatiotemporal dissection of the cell cycle with single-cell proteogenomics." https://www.nature.com/articles/s41586-021-03232-9.

The input data will be restructured for ease of future use.