SCTC-Challenge-zho_team

DREAM Single Cell Transcriptomics Challenge

The code includes three parts:

1. Sub challenge Input: dge_raw.txt, dge_normalized.txt, binarized_bdtnp.csv, geometry.txt (https://www.synapse.org/#!Synapse:syn16782360). Users should register in Synapse (https://www.synapse.org/) using email address and agree to the dataset Conditions for use (https://www.synapse.org/#!Synapse:syn15665609/wiki/583240), then they can download these files

   Code: challenge_code_1.R, challenge_code_2.R, challenge_code_3.R, challenge_utils.R.

   Output:

   • raw.data
   • normalized.data
   • geometry
   • insitu.matrix
   • insitu.genes
   • gene60, gene40, gene20
   • dm60, dm40, dm20
   • bin60, bin40, bin20
   • maxc60, maxc40, maxc20
   • sl60, sl40, sl20

2. Post sub challenge - 10 fold cross validation Input: folds_train.csv, folds_test.csv Code: post_challenge_all.R, newUtils.R Output:

   • binDist60, binDist40, binDist20

3. Scores 1, 2, 3 (https://github.com/dream-sctc/Scoring/blob/master/dream_scoring_clean.R)

   Input: output of 1, 2

   Code: estimate_all.R, estimate_util.R

   Output: results in the manuscript