intervene

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Hello. I am trying to install Intervene using conda, but haven't had any luck so far. I have tried some of the recommendations mentioned in some of the other issues,...

kyleLesack

pairwise is not working even on --test

10

Hi install latest version of intervene using git but its not working for pairwise. and by the way, using conda, its installing 0.5.8 which is not latest and does not...

unique379

total number diff in venn plot

1

``` intervene venn -i ./*.bed --output . --bedtools-options f=1,s,r --figtype png --title "precision(100%)" mv Intervene_venn.png compare_1.png sleep 3 intervene venn -i ./*.bed --output . --bedtools-options f=0.75,s,r --figtype png --title "precision(75%)"...

whiteorchid

Support for proportional venn diagrams?

12

Thanks for developing a really useful package for quickly intersecting genesets and regions. If possible, one nice addition would be to support scaling of the circles of the venn diagrams...

hvbakel

upsetr script not plotting

2

Hi, I was using the intervene UpSetR module to graph the intersect between bed files but the produced R script does not seem to plot. I get the following message...

nouratb

error when attempting to use pairwise

3

Hi, I'm trying to use pairwise with lists and I'm getting an error message. Note the everything works fine when using venn instead. Here's the command I used: `intervene pairwise...

dllahr

no tmp dir created when generating 3-way "venn" diagram

3

I get this traceback when trying to run intervene venn with 3 vcf files: ``` Traceback (most recent call last): File "/opt/anaconda3/bin/intervene", line 606, in main() File "/opt/anaconda3/bin/intervene", line 522,...

scalavision

intersect result is wrong compare to bedtools intersect

11

I compare R function intersect in GenomicRanges package(terms RI), linux bedtools intersect(LI) and your tools, find that RI is the same as LI, but some wrong in your tools. I...

StayHungryStayFool

search not working in readthedocs

1

Hi I'm not sure if this should be reported here but when I try to use the search bar in readthedocs for example: https://intervene.readthedocs.io/en/latest/search.html?q=venn&check_keywords=yes&area=default it returns 0 results, even though...

dllahr

conda install not working with existing environment python=3.7

1

Hi Thank you for building this incredibly useful tool! It has greatly improved how we are able to look at set overlap data. I ran into a problem trying to...

dllahr