EWCE

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generate_celltype_data struggling with a large matrix: "too many elements (>= 2^31) selected along dimension 1 of array"

7

## 1. Bug description When running `generate_celltype_data()` on a gene-by-cell matrix of 34807 x 786896, I get a large array error. My input object (`exp`) is `sparse DelayedMatrix object of...

ainefairbrother

bootstrap_enrichment_test throws "Error in exp_mats[[cc]][s, ] <- sort(expD[, cc]) : replacement has length zero"

11

## 1. Bug description When running EWCE with my own gene lists and single cell data, I get this error: "Error in exp_mats[[cc]][s, ]

Kfarls

Consider removing <4 gene limit

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Currently `EWCE::bootstrap_enrichment_test` doesn't let you run tests where the number of hit genes is what are the dangers of reducing the number of genes? from a stats standpoint @Al-Murphy >...

bschilder

Take marker genes from Human Cell Atlas? We don't want it to be circular Might be easiest to just pick e.g. 100 celltype specific genes, then add random genes until...

NathanSkene

How do the various methods of filtering low-expressed genes now implemented affect the results?

4

NathanSkene

NathanSkene

We’ve altered how 1:1 orthologs are defined, does this affect results? How does the stringency of the definition of orthologous affect results? (Brian can explain in more detail)

NathanSkene

Enrichment test in version 1.7.1

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## 1. Bug description Thank you for updating to provide the bootstrap probability for each gene. However, I met an error that was not seen in 1.6.0 when I performed...

forrestzhaosen

Gene-Scoring Table for Cell Type Enrichment

1

Hello, I am trying to retrieve a list of genes that contribute to the enrichment of each cell type. I came across some related issues, and I noticed that @bschilder...

pmayog

**Is your feature request related to a problem? Please describe.** When I do bootstrap enrichment tests I have for some particular usecases very strong enrichments for for example GABAergic neurons,...

KevinMarinus