greenelab/RNAseq_titration_results

Issues

• Update with published paper links

  #151 opened 2 years ago by envest
  0

• Violin plots appear like they are not violins

  #144 opened 2 years ago by envest
  5

• Compare PLIER pathways across different sample sizes

  #142 opened 2 years ago by envest
  1

• Performance difference with linear SVM using classProbs = TRUE

  #139 opened 2 years ago by envest
  0

• Add AUC, sensitivity, and specificity metrics

  #132 opened 2 years ago by envest
  0

• Try single cell integration method for normalization (fastMNN)

  #124 opened 2 years ago by envest
  0

• Implement running new normalization methods

  #125 opened 2 years ago by envest
  1

• Seurat for single cell integration

  #128 opened 2 years ago by envest
  0

• preprocessCore error

  #127 opened 2 years ago by envest
  0

• Add another normalization method: CrossNorm

  #122 opened 2 years ago by envest
  1

• Permute PLIER pathway-gene relationships

  #121 opened 2 years ago by envest
  0

• Major home page documentation update

  #99 opened 3 years ago by envest
  0

• Reconceptualize all publication plots

  #77 opened 3 years ago by envest
  0

• Diagnose and fix problems experienced with R 4.0.3

  #41 opened 3 years ago by envest
  3

• Identify pathways using PLIER

  #73 opened 3 years ago by envest
  0

• Visualize expression values before and after normalization

  #76 opened 3 years ago by envest
  4

• Allow zeros in NAToZero

  #89 opened 3 years ago by envest
  0

• DEG metrics edge cases

  #80 opened 3 years ago by envest
  1

• Add untransformed expression data as a negative control

  #85 opened 3 years ago by envest
  0

• Expand small n DEG comparison

  #74 opened 3 years ago by envest
  0

• Add metrics to evaluate DEG overlap

  #75 opened 3 years ago by envest
  0

• Predict mutation status

  #51 opened 3 years ago by envest
  2

• Update differential expression scripts for new files name structure

  #68 opened 3 years ago by envest
  2

• Move modification of BRCAClin.tsv file later in download script

  #67 opened 3 years ago by envest
  1

• Remove group column in some summary output tables

  #66 opened 3 years ago by envest
  0

• Change default values of mandatory optparse arguments to NA

  #56 opened 3 years ago by envest
  0

• Load tidyverse instead of individual tidy packages

  #59 opened 3 years ago by envest
  1

• Update BRCA clinical table in zenodo with 'subtype' column name

  #50 opened 3 years ago by envest
  3

• Use here for referencing utilities with source()

  #49 opened 3 years ago by envest
  0

• Improve readability of mutations script

  #46 opened 3 years ago by envest
  0

• Check md5 sums of downloaded files against expectation

  #43 opened 3 years ago by envest
  1

• Use optparse library for command line arguments

  #12 opened 3 years ago by jaclyn-taroni
  0

• PredictWrapper return Kappa argument

  #29 opened 3 years ago by jaclyn-taroni
  0

• Prepare GBM data for use in scripts

  #40 opened 3 years ago by envest
  0

• Move analysis to Docker image

  #18 opened 4 years ago by jaclyn-taroni
  0

• Combine prediction functions

  #19 opened 8 years ago by jaclyn-taroni
  0

• Restructure reconstruction analyses

  #20 opened 8 years ago by jaclyn-taroni
  0