Quickstart

digraph {
  rankdir=TB;
  abundance [label="<f0> TMM(TPM)|<f1> counts|<f2> transcript metrics", shape=record];
  de [label="<f0> log2(fold-change)|<f1> p-value", shape=record];
  qc [label="<f0> nucleotide metrics|<f1> genotype metrics", shape=record];
  index [label="<f0> salmon index|<f1> gene-transcript mapping|<f2> transcript/intron/intergene models", shape=record];
  "config.json" -> "pisces index" [arrowhead=none];
  "metadata.csv" -> "pisces submit" [arrowhead=none];
  "metadata.csv" -> "pisces summarize-expression" [arrowhead=none];
  "metadata.csv" -> "pisces summarize-qc" [arrowhead=none];
  "contrasts.csv" -> "pisces summarize-expression" [arrowhead=none];
  "pisces submit" -> "pisces summarize-expression";
  "pisces submit" -> "pisces summarize-qc";
  "pisces summarize-expression" -> abundance;
  "pisces summarize-expression" -> de;
  "pisces summarize-qc" -> qc;
  "pisces index" -> index;
  index -> "pisces submit";
  }

Fig. 9 Overview of PISCES workflow, demonstrating configuration file inputs and descriptions of processes and outputs for each PISCES subcommand (index, submit, summarize-expression and summarize-qc).

Publication

The manuscript is available on bioRxiv and the latest version can be viewed in this documentation: PISCES: a package for rapid quantitation and quality control of large scale mRNA-seq datasets.

Matthew D Shirley, Viveksagar K Radhakrishna, Javad Golji, Joshua M Korn. PISCES: a package for rapid quantitation and quality control of large scale mRNA-seq datasets. bioRxiv. 2020.

Development

Pull requests and issues are welcomed on the pisces Github repository.