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NathanSkene
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EWCE
Expression Weighted Celltype Enrichment. See the package website for up-to-date instructions on usage.
https://nathanskene.github.io/EWCE/index.html
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How do I analyze a Seurat object?
#94
jmzhang1911
closed
2 months ago
2
Errors when running a conditional analysis on level 2 data
#93
JoshHarveyGit
closed
3 months ago
1
Keep popular fails with duplicate gene names
#92
rbutleriii
closed
3 months ago
7
generate_celltype_data struggling with a large matrix: "too many elements (>= 2^31) selected along dimension 1 of array"
#91
ainefairbrother
opened
7 months ago
7
How can I extract a list of genes that drive the (significant) enrichment for a particular cell type?
#90
KevinMarinus
closed
6 months ago
6
rworkflows: Set `docker_registry: docker.io`
#89
bschilder
closed
8 months ago
0
Dendrogram not reordering cell types in plot
#88
Al-Murphy
closed
8 months ago
1
could not find function "read_celltype_data"
#87
ashrma314
closed
8 months ago
14
bootstrap_enrichment_test throws "Error in exp_mats[[cc]][s, ] <- sort(expD[, cc]) : replacement has length zero"
#86
Kfarls
opened
9 months ago
1
generate_bootstrap_plots gives error "in check_ewce_genelist_inputs"
#85
SuMi300
closed
8 months ago
5
GHA Linux: deploy website
#84
bschilder
closed
8 months ago
1
Remove dead branches
#83
bschilder
closed
1 year ago
1
generate_bootstrap_plots gives error "in check_ewce_genelist_inputs"
#82
SuMi300
closed
1 year ago
1
Error using DESeq2 Wald test for `drop_uninformative_genes()`
#81
cyouh95
closed
1 year ago
2
background not appropriate when the `sct_data` was previously converted from another species.
#80
bschilder
closed
1 year ago
3
Consider removing <4 gene limit
#79
bschilder
opened
1 year ago
2
Enrichment test in version 1.7.1
#78
forrestzhaosen
opened
1 year ago
2
Driver gene identification
#77
forrestzhaosen
closed
1 year ago
15
Extracting genes driving the enrichment and their mean bootstrap expression
#76
iscastanho
closed
1 year ago
3
Issue with background gene lists and orthogene
#75
Al-Murphy
closed
1 year ago
2
`EWCE::standardise_ctd`: not enforcing "specificity_quantiles" matrix
#74
bschilder
closed
1 year ago
4
`standardise_ctd`: matrices not getting converted to sparse
#73
bschilder
closed
1 year ago
1
`filter_ctd_genes`: handle new CTD format
#72
bschilder
closed
1 year ago
0
Appropiate background genes for GC & length correction
#71
xoelmb
closed
1 year ago
8
Cannot install EWCE > 1.2 with R 4.1 or R 4.2 (incompatible dependencies)
#70
iscastanho
closed
2 years ago
4
`genelistSpecies` not inherited by `prepare_genesize_control_network()` in `bootstrap_enrichment_test()`
#69
RHReynolds
closed
2 years ago
3
generate_celltype_data with raw or SCTransformed data
#68
artemisiat
closed
2 years ago
4
Proportional expression of individual hit genes
#67
h1hui
closed
2 years ago
1
Error with generate_bootstrap_plots
#66
h1hui
closed
2 years ago
3
Run Cell-type Enrichment Tests on Two Annotation Levels
#65
h1hui
closed
2 years ago
3
Use CTD file after generate_celltype_data
#64
h1hui
closed
2 years ago
0
Expression in cell type (%)
#63
h1hui
closed
2 years ago
7
Update param documentation - groupName in generate_celltype_data
#62
Al-Murphy
closed
2 years ago
0
1:1 ortholog mapping using orthogene and One2One yields different results
#61
KittyMurphy
closed
2 years ago
4
Choose what we're going to take as the 'true positive' results
#60
NathanSkene
opened
2 years ago
0
How do the various methods of filtering low-expressed genes now implemented affect the results?
#59
NathanSkene
opened
2 years ago
4
How much does parallelisation increase speed?
#58
NathanSkene
opened
2 years ago
0
How does 1:1 ortholog definition affect results?
#57
NathanSkene
opened
2 years ago
0
Does significance of an association always increase as the complexity of the scRNA-seq dataset increases
#56
NathanSkene
closed
1 year ago
1
EWCE:::is_celltypedataset. Does not state why the cell type data is not valid.
#55
roxyisat-rex
closed
1 year ago
1
Docker issues
#54
bschilder
closed
2 years ago
2
Add comparison of `orthogene` and `mouse_to_human_homologs`
#53
bschilder
closed
2 years ago
0
Don't run tests on 32-bit Windows
#52
bschilder
closed
2 years ago
0
Parallelise `bootstrap_enrichment_test`
#51
bschilder
closed
2 years ago
2
Build tests must confirm that EWCE docker image works as expected
#50
NathanSkene
closed
2 years ago
2
Improve GHA workflow checks
#49
bschilder
closed
2 years ago
1
Automatic DockerHub builds
#48
bschilder
closed
2 years ago
1
EWCE 2.0
#47
bschilder
closed
2 years ago
10
Extend EWCE to handle any species
#46
bschilder
closed
2 years ago
1
Make function arguments explicit
#45
bschilder
closed
2 years ago
1
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