Shams

Make error: Error 2 on lumpy-sv

1

Hi, I am getting constant error during the installation of speedseq. I have git cloned the speedseq and tried the make command after installing all the dependencie `git clone --recursive...

Pseudo time as function of a predefined group of genes

3

Is it possible to plot the cells as a function of a list of genes?

cell-cycle & mitochondrial regression

2

Is there any way to use cell-cycle & mitochondrial fraction regressed data for PHATE? Thanks, Shams

In my data set (114k cells 100 gene sets and 10 cell types), `spc.est_spectra` stops after some epochs without any error message. Most of the outputs are being populated in...

Imputing integrated data

1

Hi, Thank you for the nice tool. Is there any way to use ALRA in integrated data?. Currently if we use ALRA, it seems to be masking the difference in...

Is there any way to increase sql column limits like using `SQLITE_MAX_COLUMN`. Currently it works on default 2000 one. Thanks, Shams

Image based QC prior to aggregate_profiles

4

Are there any QC procedure that could be done prior to aggregating well. In my case any images that have less cell dense region would create an artifact as the...