PNNL-CompBio/spammR

Issues

• Check about incorporating mouse geneset databases directly into leapR; making sure spammR::enrich_ORA() still runs.

  #28 opened a month ago by HarkiratSohi
  0

• Load Pancreas dataset with tissue image(s) and metadata file

  #27 opened a month ago by HarkiratSohi
  0

• Resolve loading of other packages used by spammR

  #26 opened a month ago by HarkiratSohi
  0

• Add to TestData folder; show functions work using test data.

  #25 opened a month ago by HarkiratSohi
  0

• Turn spammR into Bioconductor package

  #24 opened a month ago by HarkiratSohi
  0

• Add spatial_enrichmentInSets.R

  #4 opened a month ago by HarkiratSohi
  1

• Add a module (set of functions) for imputing missing data

  #21 opened a month ago by HarkiratSohi
  1

• Add functions for distance based analysis

  #20 opened a month ago by HarkiratSohi
  1

• Add functions for comparing proteomics and MERFISH data

  #22 opened a year ago by HarkiratSohi
  0

• Functions for analyzing MERFISH data

  #23 opened a year ago by HarkiratSohi
  0

• Create a version of readme using brain proteomics data as an example

  #18 opened a year ago by HarkiratSohi
  0

• Add functions for Network graph visualizations

  #8 opened a year ago by HarkiratSohi
  0

• Add a function for exporting data from the MERFISH package

  #19 opened a year ago by HarkiratSohi
  0

• Add a function for creating volcano plots for visualizing results from spatialDiffEx.R

  #5 opened a year ago by HarkiratSohi
  0

• spatialDiffEx.R - add results as an assay in output spe object

  #12 opened a year ago by HarkiratSohi
  1

• Make spatialDiffEx.R compatible with SPE object; allow more generalization of input parameters

  #2 opened a year ago by HarkiratSohi
  3

• Function for carrying out PCA analysis & clustering and spatial plotting of samples, color-coded by cluster color.

  #7 opened a year ago by HarkiratSohi
  1

• Provide a helper function for converting IDs of the form sp|Z|X_Y to gene names

  #6 opened a year ago by HarkiratSohi
  0

• Add pathway_spatialExpCompare.R

  #3 opened a year ago by HarkiratSohi
  0