Vladimir (Vlad) Kiselev

Check random seed

7

Looks like the seed is changed somewhere in the code, so sometimes results cannot be reproduced...

Allow users to define a different colour palette for annotation colours on all heatmaps.

At the moment these calculations are too slow.

basic_string::substr error when running dropEst

3

Hello, this may be related to #43 but I get the following error when running dropEst: ``` dropest -m -w -g Homo_sapiens.GRCh38.91.gtf -c indrop_v1_2.xml -o TAM103018-001_S1_L001.est Aligned.sortedByCoord.out.bam Run: 02/04/2019 17:16:44....

Azure batch run in Tower gets stuck in Submitted state

22

# Bug report ## Expected behavior and actual behavior Expected: Completed run should get either in `Failed` or `Succeeded` state. Actual: Completed run is stuck in `Submitted` state even though...

https://github.com/pkathail/magic/blob/develop/R/run_magic.R

Users have to have the latest version installed on their machines

http://bioconductor.org/packages/release/bioc/html/SIMLR.html

add --target-file argument

1

Adding the `--target-file` argument requires an extra input to this module - a `bed` file. This commit adds the `bed` file input to the module.