hms-dbmi/dseqr

Issues

• Compatibility with Seurat v5 Objects

  #205 opened 8 months ago by afonsoguerra
  2

• validate single cell drug matching

  #121 opened 3 years ago by alexvpickering
  0

• allow gene-cell labeling

  #148 opened 3 years ago by alexvpickering
  0

• Add auto-detection of strandedness for paired-end bulk data

  #160 opened 3 years ago by alexvpickering
  0

• remove duplicates in gs.list

  #166 opened 3 years ago by alexvpickering
  0

• Change custom queries to allow csv upload

  #165 opened 4 years ago by alexvpickering
  0

• Add documentation page to web app

  #147 opened 5 years ago by alexvpickering
  1

• move away from goana/kegga to cameraPR for pathway analysis

  #157 opened 5 years ago by alexvpickering
  0

• show effect sizes for custom queries

  #164 opened 5 years ago by alexvpickering
  0

• Add conversion function from crossmeta --> drugseqr

  #161 opened 5 years ago by alexvpickering
  0

• use group aware filterByExpr

  #163 opened 5 years ago by alexvpickering
  0

• allow for "invalid" group names

  #162 opened 5 years ago by alexvpickering
  0

• improve error message when kallisto index not built

  #159 opened 5 years ago by alexvpickering
  0

• couldn't add 17th replicates for covid19 quantification

  #158 opened 5 years ago by alexvpickering
  1

• Allow labeling of bulk samples by download/upload of csv of sample metadata

  #156 opened 5 years ago by alexvpickering
  1

• Download results button not disabled during differential expression analysis

  #134 opened 5 years ago by alexvpickering
  0

• Fix ShinyProxy config for mobile

  #155 opened 5 years ago by alexvpickering
  0

• convert Seurat pipeline to SingleCellExperiment

  #154 opened 5 years ago by alexvpickering
  0

• directory selection dialogue auto opens after adding single cell dataset

  #140 opened 5 years ago by alexvpickering
  0

• move import of new sc data to Single Cell tab and rename Datasets tab to Bulk

  #151 opened 5 years ago by alexvpickering
  0

• adjust for custom number of surrogate variables

  #152 opened 5 years ago by alexvpickering
  0

• adjust/model paired samples for bulk plots and analyses

  #153 opened 5 years ago by alexvpickering
  0

• allow overwriting of integrated single cell datasets

  #149 opened 5 years ago by alexvpickering
  0

• move query/drug gene plots to Drugs tab

  #150 opened 5 years ago by alexvpickering
  2

• show perturbation effect size as arrow in Pathways tab

  #146 opened 5 years ago by alexvpickering
  1

• Implement cell type deconvolution of bulk datasets

  #139 opened 5 years ago by alexvpickering
  4

• add tooltips to inputs with buttons

  #145 opened 5 years ago by alexvpickering
  1

• add ability to download data for gene and cell-type deconvolution plotlys

  #144 opened 5 years ago by alexvpickering
  0

• add ability to download data for single cell plots

  #143 opened 5 years ago by alexvpickering
  0

• fix single cell dataset selection in Pathways tab

  #142 opened 5 years ago by alexvpickering
  0

• Seperate single cell cluster metadata from data object

  #141 opened 5 years ago by alexvpickering
  1

• Move custom gene set in Pathways tab to Datasets tab

  #138 opened 5 years ago by alexvpickering
  1

• show drug effect size in Pathways tab

  #137 opened 5 years ago by alexvpickering
  1

• Some genes not showing up in custom gene set plot

  #136 opened 5 years ago by alexvpickering
  0

• permit exploring original labels after single cell sample integration

  #135 opened 5 years ago by alexvpickering
  0

• setup example app

  #130 opened 5 years ago by alexvpickering
  0

• reset Datasets tab after scseq quantification

  #131 opened 5 years ago by alexvpickering
  0

• Quantification double check model doesn't adjust wording for end type

  #133 opened 5 years ago by alexvpickering
  0

• allow loading CellRanger processed single cell data

  #132 opened 5 years ago by alexvpickering
  0

• Determine if RNA-Seq or microarray gives better drug query results against CMAP02

  #127 opened 5 years ago by alexvpickering
  1

• Determine if kallisto or salmon quantification gives better CMAP02 queries

  #128 opened 5 years ago by alexvpickering
  1

• put together instructions to setup on AWS

  #123 opened 5 years ago by alexvpickering
  0

• Allow filtering negative/positive results when sorted by absolute correlation

  #129 opened 5 years ago by alexvpickering
  0

• download CMAP02/L1000 pert query results as needed

  #126 opened 5 years ago by alexvpickering
  0

• allow processing single cell data from app

  #122 opened 5 years ago by alexvpickering
  0

• show MDS plot for bulk rna-seq samples

  #125 opened 5 years ago by alexvpickering
  0

• show bulk/single cell and dataset for selected analysis

  #124 opened 5 years ago by alexvpickering
  0

• derive pval/fdr more efficiently

  #118 opened 5 years ago by alexvpickering
  1

• show genetic perts most similar to drugs and vice versa

  #120 opened 5 years ago by alexvpickering
  1

• only transfer labels for high confidence clusters

  #119 opened 5 years ago by alexvpickering
  0