Sam Bryce-Smith issues

Results 5 issues of


                                            Sam Bryce-Smith

pr.subtract - strandedness=None does not compare PyRanges on the same strand (even if both stranded)

Example: ``` import pyranges as pr gr1 = pr.from_dict({"Chromosome": ["chr1"], "Start": [10], "End": [20], "Strand": ["+"]}) gr2 = pr.from_dict({"Chromosome": ["chr1"], "Start": [10], "End": [25], "Strand": ["-"]}) gr1.stranded # True gr2.stranded...

pr.features.introns(by="transcript") returns empty PyRanges when passed a PyRanges containing exons only

Hi Endre, Not quite sure if this lands as a bug/feature request so I'll leave that up to you to decide. I'd like to be able to use the introns...

Setup fails with pip install

Hi, I've tried to install iCount through pip and I'm getting the following error. It is consistent across using pip or pip3 to install (my python versions are 2.7 &...

https://rnajournal.cshlp.org/content/29/12/1839.long - APAeval - identification and quantification of alternative polyadenylation sites from bulk RNA-seq data

Bit of shameless self promotion on behalf of the team, but think it's a nice fit into the repo! With APAeval we aimed to benchmark tools that perform identification and...

-ptf option - recommended input & implementation details?

Hi, I'm interested in using StringTie finding novel last exons and the recently added `-ptf` option seems quite relevant. I have a couple of questions regarding recommended input sites and...