User: endrebak

gravatar for endrebak
endrebak560
Reputation:
560
Status:
Trusted
Location:
Website:
https://github.com/end...
Last seen:
3 hours ago
Joined:
1 year ago
Email:
b***************@gmail.com

https://www.ntnu.edu/employees/endrebak

https://github.com/endrebak

 

Posts by endrebak

<prev • 72 results • page 1 of 8 • next >
0
votes
1
answer
846
views
1
answers
Comment: C: generate fastq with bed file
... That generates a fasta, not a fastq :) ...
written 4 days ago by endrebak560
0
votes
9
answers
4.3k
views
9
answers
Comment: C: How Do We Discourage Ad-Hoc Bioinformatic Analyses?
... Snakemake all the things ...
written 24 days ago by endrebak560
1
vote
3
answers
15k
views
3
answers
Comment: C: How To Convert Gencode Gtf Into Bed Format ?
... Thanks, changed my answer :) ...
written 4 months ago by endrebak560
0
votes
1
answer
992
views
1
answers
Comment: C: epic: new ChIP-Seq caller based on the SICER algorithm
... If you want to discuss bam-support, please do it here: https://github.com/endrebak/epic/issues/44 ...
written 6 months ago by endrebak560
0
votes
1
answer
992
views
1
answers
Comment: C: epic: new ChIP-Seq caller based on the SICER algorithm
... You can scroll down Istvan 🙂 ...
written 6 months ago by endrebak560
0
votes
1
answer
992
views
1
answers
Comment: C: epic: new ChIP-Seq caller based on the SICER algorithm
... You will probably rerun the analyses many times. Having to run a time-consuming conversion step (the most time-consuming one in the algorithm) each time would be silly. It is also IO-intensive so parallell execution would not help much. I am not just writing epic but a lot of helper scripts for ChI ...
written 6 months ago by endrebak560
0
votes
1
answer
277
views
1
answers
Comment: C: Create bigwigs in python?
... It seems like bw.addEntries would take four enormous lists if I know all the entries upfront. I guess I should chunk the data and add a 1000 entries at a time... ...
written 6 months ago by endrebak560
0
votes
1
answer
277
views
1
answers
Comment: C: Create bigwigs in python?
... Wonderful, thanks for your effort! Python3 even <3 ...
written 6 months ago by endrebak560
3
votes
1
answer
277
views
1
answer
Create bigwigs in python?
... I want to create bigwigs in Python. Is there a library that can do this? Two ways of doing it that I'd rather avoid: Currently I use rpy2 with rtracklayer and genomicranges through bioconda. This works, but is a bit heavy on the dependencies. Example code: https://github.com/endrebak/epic/blob/25 ...
chip-seq written 6 months ago by endrebak560
0
votes
4
answers
16k
views
4
answers
Answer: A: How To Write Data In A Granges Object To A Bed File.
... If you only have one metadata column and you would like to keep it, this modification of Devon Ryan's answer works: df <- data.frame(seqnames=seqnames(gr), starts=start(gr)-1, ends=end(gr), names=c(rep(".", length(gr))), scores=elementMetadata(gr)[,1], strands=strand(gr) ...
written 7 months ago by endrebak560

Latest awards to endrebak

Teacher 4 months ago, created an answer with at least 3 up-votes. For A: How To Convert Gencode Gtf Into Bed Format ?
Voter 7 months ago, voted more than 100 times.
Scholar 8 months ago, created an answer that has been accepted. For A: Given a link that displays genome browser data, how do I download a pdf using a
Student 8 months ago, asked a question with at least 3 up-votes. For Fast datastructure to get counts of overlapping reads per nucleotide (!) in Python?
Supporter 11 months ago, voted at least 25 times.
Appreciated 12 months ago, created a post with more than 5 votes. For epic: new ChIP-Seq caller based on the SICER algorithm
Autobiographer 12 months ago, has more than 80 characters in the information field of the user's profile.
Appreciated 12 months ago, created a post with more than 5 votes. For epic: new ChIP-Seq caller based on the SICER algorithm
Student 12 months ago, asked a question with at least 3 up-votes. For epic: new ChIP-Seq caller based on the SICER algorithm
Commentator 12 months ago, created a comment with at least 3 up-votes. For C: SICER raw data

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.3.0
Traffic: 1447 users visited in the last hour