DailyDreaming/load-project

Issues

• Create QC plots for matrices added this week

  #107 opened 5 years ago by hannes-ucsc
  2

• Import SCXA projects

  #111 opened 5 years ago by hannes-ucsc
  1

• Decide what to do with the GEO projects that have an HCA matrix

  #121 opened 5 years ago by hannes-ucsc
  1

• Reconcile differences between methods to generate cell counts

  #113 opened 5 years ago by theathorn
  3

• Missing header line in some barcodes.tsv.gz and genes.tsv.gz files

  #142 opened 5 years ago by dsotirho-ucsc
  3

• Extend cell_count.py to count genes and compare diff counting method results

  #144 opened 5 years ago by dsotirho-ucsc
  0

• Eliminate `cell_counts.json`

  #122 opened 5 years ago by hannes-ucsc
  0

• Survey additional GEO and SCXA projects

  #92 opened 5 years ago by hannes-ucsc
  3

• Upload breaks if too many files (100+?)

  #54 opened 5 years ago by DailyDreaming
  1

• Generate skunk bundles for HCA prod projects

  #94 opened 5 years ago by theathorn
  1

• Review skipped GEO matrices

  #95 opened 5 years ago by theathorn
  1

• Handle latin1 Excel quotes in GSE127969_counts_TPM_ALL.csv.gz

  #114 opened 5 years ago by theathorn
  1

• Missing metadata for certain GEO projects

  #118 opened 5 years ago by hannes-ucsc
  0

• Path to converted per-cell matrices should reflect complete path relative to `geo` dir

  #123 opened 5 years ago by hannes-ucsc
  7

• Row length assertions fire

  #145 opened 5 years ago by hannes-ucsc
  0

• Standardize width of QC plots to 600 pixels

  #141 opened 5 years ago by theathorn
  1

• Move tsne script into load-project repo.

  #135 opened 5 years ago by theathorn
  1

• Cite tsne plot sources.

  #117 opened 5 years ago by DailyDreaming
  1

• Log mtx inconsistencies in count_cells.py

  #108 opened 5 years ago by hannes-ucsc
  0

• Add gene names to matrices converted from CSV

  #112 opened 5 years ago by theathorn
  0

• get_target_project_dirs does not work with UUIDS

  #133 opened 5 years ago by nadove-ucsc
  1

• First argument to IndividualCellFiles constructor should be as specific as possible

  #125 opened 5 years ago by hannes-ucsc
  2

• Fix matrices that break QC plots

  #96 opened 5 years ago by nadove-ucsc
  1

• Missing file extensions in h5 conversion output

  #132 opened 5 years ago by nadove-ucsc
  1

• atomic_gzip_file truncates file contents

  #131 opened 5 years ago by nadove-ucsc
  1

• Use globs to compact the explicit lists of paths in convert_matrices

  #102 opened 5 years ago by hannes-ucsc
  0

• Add support for static matrices and metadata to `make report`

  #120 opened 5 years ago by hannes-ucsc
  0

• Trim whitespace from csv value when creating mtx

  #129 opened 5 years ago by dsotirho-ucsc
  0

• Add gene names to matrices converted from H5

  #105 opened 5 years ago by hannes-ucsc
  1

• Create individual users on the instance

  #103 opened 5 years ago by hannes-ucsc
  0

• Parallelize MTX generation

  #86 opened 5 years ago by hannes-ucsc
  0

• `make matrices` fails for GSE113197

  #119 opened 5 years ago by hannes-ucsc
  1

• Replace uses of `path.as_posix()` with `str(path)`

  #101 opened 5 years ago by hannes-ucsc
  0

• No metadata for 5016f45e-b86a-57ce-984e-a50605641d08

  #72 opened 5 years ago by hannes-ucsc
  5

• Add ability to limit working set for all scripts

  #87 opened 5 years ago by hannes-ucsc
  2

• Make `make assets` idempotent

  #91 opened 5 years ago by hannes-ucsc
  0

• Improve idempotency for matrix zip generation

  #106 opened 5 years ago by jessebrennan
  0

• Write sanity checker

  #82 opened 5 years ago by hannes-ucsc
  0

• Beef up instance

  #85 opened 5 years ago by hannes-ucsc
  1

• Broken links to external resources

  #57 opened 5 years ago by DailyDreaming
  4

• Make Azul indexer handle a mix of skunk and normal bundles

  #93 opened 5 years ago by hannes-ucsc
  0

• Improve idempotence on convert_matrices.py

  #88 opened 5 years ago by hannes-ucsc
  1

• Gzipped files contain temp name

  #81 opened 5 years ago by jessebrennan
  0

• Not all projects are gzipped

  #66 opened 5 years ago by nadove-ucsc
  1

• Warn when matrix conversion code is skipped

  #78 opened 5 years ago by jessebrennan
  1

• Disable unnecessary HEAD requests for matrices

  #73 opened 5 years ago by jessebrennan
  0

• DB shows 47 matrices while instance only stores 46

  #75 opened 5 years ago by hannes-ucsc
  4

• Create statistics for cumulative cell counts over time

  #60 opened 5 years ago by theathorn
  3

• Why does the # of specimens match the # of projects

  #48 opened 5 years ago by hannes-ucsc
  0

• Consider placing each matrix as a separate file in DSS

  #49 opened 5 years ago by hannes-ucsc
  0