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hms-dbmi
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dseqr
single-cell and bulk RNA-seq analyses from counts → pathways → drug candidates.
https://docs.dseqr.com
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improve error message when kallisto index not built
#159
alexvpickering
closed
4 years ago
0
couldn't add 17th replicates for covid19 quantification
#158
alexvpickering
closed
4 years ago
1
move away from goana/kegga to cameraPR for pathway analysis
#157
alexvpickering
closed
4 years ago
0
Allow labeling of bulk samples by download/upload of csv of sample metadata
#156
alexvpickering
closed
4 years ago
1
Fix ShinyProxy config for mobile
#155
alexvpickering
closed
4 years ago
0
convert Seurat pipeline to SingleCellExperiment
#154
alexvpickering
closed
4 years ago
0
adjust/model paired samples for bulk plots and analyses
#153
alexvpickering
closed
4 years ago
0
adjust for custom number of surrogate variables
#152
alexvpickering
closed
4 years ago
0
move import of new sc data to Single Cell tab and rename Datasets tab to Bulk
#151
alexvpickering
closed
4 years ago
0
move query/drug gene plots to Drugs tab
#150
alexvpickering
closed
4 years ago
2
allow overwriting of integrated single cell datasets
#149
alexvpickering
closed
4 years ago
0
allow gene-cell labeling
#148
alexvpickering
closed
3 years ago
0
Add documentation page to web app
#147
alexvpickering
closed
4 years ago
1
show perturbation effect size as arrow in Pathways tab
#146
alexvpickering
closed
4 years ago
1
add tooltips to inputs with buttons
#145
alexvpickering
closed
4 years ago
1
add ability to download data for gene and cell-type deconvolution plotlys
#144
alexvpickering
closed
4 years ago
0
add ability to download data for single cell plots
#143
alexvpickering
closed
4 years ago
0
fix single cell dataset selection in Pathways tab
#142
alexvpickering
closed
4 years ago
0
Seperate single cell cluster metadata from data object
#141
alexvpickering
closed
4 years ago
1
directory selection dialogue auto opens after adding single cell dataset
#140
alexvpickering
closed
4 years ago
0
Implement cell type deconvolution of bulk datasets
#139
alexvpickering
closed
4 years ago
4
Move custom gene set in Pathways tab to Datasets tab
#138
alexvpickering
closed
4 years ago
1
show drug effect size in Pathways tab
#137
alexvpickering
closed
4 years ago
1
Some genes not showing up in custom gene set plot
#136
alexvpickering
closed
4 years ago
0
permit exploring original labels after single cell sample integration
#135
alexvpickering
closed
4 years ago
0
Download results button not disabled during differential expression analysis
#134
alexvpickering
closed
4 years ago
0
Quantification double check model doesn't adjust wording for end type
#133
alexvpickering
closed
4 years ago
0
allow loading CellRanger processed single cell data
#132
alexvpickering
closed
4 years ago
0
reset Datasets tab after scseq quantification
#131
alexvpickering
closed
4 years ago
0
setup example app
#130
alexvpickering
closed
4 years ago
0
Allow filtering negative/positive results when sorted by absolute correlation
#129
alexvpickering
closed
4 years ago
0
Determine if kallisto or salmon quantification gives better CMAP02 queries
#128
alexvpickering
closed
4 years ago
1
Determine if RNA-Seq or microarray gives better drug query results against CMAP02
#127
alexvpickering
closed
4 years ago
1
download CMAP02/L1000 pert query results as needed
#126
alexvpickering
closed
4 years ago
0
show MDS plot for bulk rna-seq samples
#125
alexvpickering
closed
4 years ago
0
show bulk/single cell and dataset for selected analysis
#124
alexvpickering
closed
4 years ago
0
put together instructions to setup on AWS
#123
alexvpickering
closed
4 years ago
0
allow processing single cell data from app
#122
alexvpickering
closed
4 years ago
0
validate single cell drug matching
#121
alexvpickering
closed
3 years ago
0
show genetic perts most similar to drugs and vice versa
#120
alexvpickering
closed
4 years ago
1
only transfer labels for high confidence clusters
#119
alexvpickering
closed
5 years ago
0
derive pval/fdr more efficiently
#118
alexvpickering
closed
4 years ago
1
add option to show queried cmap/l1000 genes
#117
alexvpickering
closed
5 years ago
0
Describe additional information for various inputs
#116
alexvpickering
closed
5 years ago
0
allow custom gene sets
#115
alexvpickering
closed
5 years ago
0
sort by absolute correlation for L1000 genetic perts
#114
alexvpickering
closed
5 years ago
0
don't filter non-expressed genes
#113
alexvpickering
closed
3 years ago
0
allow custom query signature
#112
alexvpickering
closed
4 years ago
0
show L1000 genetic perts as seperate drug study
#111
alexvpickering
closed
5 years ago
0
add genecards external link for genetic/ligand perts
#110
alexvpickering
closed
5 years ago
0
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