nroak

Feature Request: Linkage analysis?

1

I'm definitely pushing it too far, but is it possible to implement linkage analysis using Slivar? If you already have alternate tools that you or others have developed, can you...

ENH: add support for annovar annotations

6

I was trying to use [ANNOVAR](http://annovar.openbioinformatics.org/en/latest/) annotated VCF with the Slivar comphet script. I got the following error: >[noak@nodecn201 cohort_level]$ ~/resources/slivar/slivar compound-hets \ > -v $family.rare.comphet_int2.vcf \ > -f "Gene.refGene"...

I'm interested in defining column separator for -c option in bedtools merge. I have a bedj file where the 4th column of input file has characters that are automatically detected...

How to add cats in legend?

1

I'm running a simple point plotting with this package. I would like to add this to the legend but since I'm not using any aesthetic, legend doesn't show up. `p...

PanicException: called Option::unwrap() on a None value

14

### Setup I am reporting a problem with GSEApy version, Python version, and operating system as follows: ```python import sys; print(sys.version) import platform; print(platform.python_implementation()); print(platform.platform()) import gseapy; print(gseapy.__version__) ``` >...

I am posting this issue since the previously open issue didn't get any responses. I can't get past this error or debug it on my own. I'm using the latest...

Installation error

1

When I try to install the package from R, I get the following error: ``` devtools::install_github('tengfei-emory/scBatch') Downloading GitHub repo tengfei-emory/scBatch@master ✓ checking for file ‘/private/var/folders/xy/0mtz2jx51cj6n6z7b0c01b01qr2lbw/T/Rtmpnvjh6U/remotes14cb01d143898/tengfei-emory-scBatch-97fca94/DESCRIPTION’ ... ─ preparing ‘scBatch’: ✓...

I'm using [this tutorial](https://github.com/theislab/scanpy_usage/blob/master/171111_SPRING_export/SPRING_export.ipynb) for exporting adata object to SPRING input. First suggestion to update this tutorial, I had to modify this slightly per the updates in the command: `sc.external.exporting.spring_project(adata,...

I'm writing to make a feature request for an alternate representation of the heatmap as a dotplot grid. Please consider the examples below depending on the level of effort required...

When I download the tool and run it on my base conda environment, I'm getting the following error. ``` python oncotree_to_oncotree.py -i disease_code.oncotree.txt -o disease_code.oncotree.new.txt -s oncotree_2018_05_01 -t oncotree_2020_10_01 Traceback...