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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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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
5 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
try psuedo bulk counts for single cell analysis
#109
alexvpickering
closed
5 years ago
0
cluster colours are indistinguishable when too many clusters
#108
alexvpickering
closed
5 years ago
0
allow downloading csv of all gene expression values
#107
alexvpickering
closed
5 years ago
0
show top differentially expression genes as first result
#106
alexvpickering
closed
5 years ago
0
indicate that single cell pathway analysis is running
#105
alexvpickering
closed
5 years ago
0
get pathway results for single cell data
#104
alexvpickering
closed
5 years ago
0
add link out to genes in pathway plot
#103
alexvpickering
closed
5 years ago
0
add link out to KEGG pathway page
#102
alexvpickering
closed
5 years ago
0
plot expression values for selected analysis for genes in selected pathway
#101
alexvpickering
closed
5 years ago
0
select analysis and pathway in Pathways tab
#100
alexvpickering
closed
5 years ago
0
run pathway analysis after differential expression in Datasets tab
#99
alexvpickering
closed
5 years ago
0
run pathway analysis on bulk RNA-seq data
#98
alexvpickering
closed
5 years ago
0
adapt PADOG to RNA-Seq
#97
alexvpickering
closed
5 years ago
1
Feature request: show average correlation in drug table
#96
alexvpickering
closed
5 years ago
0
show rank of drug in table
#95
alexvpickering
closed
5 years ago
0
show cell type along with cell line in Drugs tab
#94
alexvpickering
closed
5 years ago
1
Correlation point locations are incorrect
#93
alexvpickering
closed
5 years ago
0
possibly incorrect concatenation of vendor names in L1000
#92
alexvpickering
closed
5 years ago
0
make app run bulk rna-seq analysis
#91
alexvpickering
closed
5 years ago
0
incorporate drug search portion of app
#90
alexvpickering
closed
5 years ago
3
option to change pt.size in explore_scseq_clusters
#89
alexvpickering
closed
5 years ago
0
option to add jitter in explore_scseq_clusters
#88
alexvpickering
closed
5 years ago
0
allow integration of datasets in explore_scseq_clusters
#87
alexvpickering
closed
5 years ago
1
implement selecting dataset for explore_scseq_clusters
#86
alexvpickering
closed
5 years ago
0
make explore_scseq_clusters available for Alexi/Grant online
#85
alexvpickering
closed
5 years ago
1
allow renaming of cluster in explore_scseq_clusters
#84
alexvpickering
closed
5 years ago
0
switch from tsne to umap
#83
alexvpickering
closed
5 years ago
0
indicate significance of marker genes
#82
alexvpickering
closed
3 years ago
3
make non-marker genes available in explore_scseq_clusters
#81
alexvpickering
closed
5 years ago
0
allow comparison to specific cluster
#80
alexvpickering
closed
5 years ago
0
switch from salmon to kallisto
#79
alexvpickering
closed
5 years ago
0
download healthy public scRNA-seq lung data
#78
alexvpickering
closed
3 years ago
0
update to Salmon 0.14
#77
alexvpickering
closed
5 years ago
1
Seurat SCTransform corrected log-normalized counts are not scaled appropriately
#76
alexvpickering
closed
5 years ago
7
get single cell gex signature for connectivity mapping
#75
alexvpickering
closed
5 years ago
1
Seurat integration can improve and deteriorate clustering
#74
alexvpickering
closed
3 years ago
0
default clusters from Seurat can seem strange
#73
alexvpickering
closed
3 years ago
1
use appropriate data for marker gene detection and visualisation
#72
alexvpickering
closed
5 years ago
0
compare markers for subclusters
#71
alexvpickering
closed
5 years ago
0
compare markers for a cluster between samples
#70
alexvpickering
closed
5 years ago
0
lots of clusters results in button wrapping
#69
alexvpickering
closed
5 years ago
0
Seurat marker row names are not gene names
#68
alexvpickering
closed
5 years ago
0
adapt pipeline to use Seurat
#67
alexvpickering
closed
5 years ago
0
add Wikipedia link to explore_scseq_clusters
#66
alexvpickering
closed
5 years ago
0
show BioGPS data for single-cell cluster identification
#65
alexvpickering
closed
5 years ago
0
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