User: rbronste

gravatar for rbronste
rbronste150
Reputation:
150
Status:
Trusted
Location:
Last seen:
1 week ago
Joined:
10 months, 1 week ago
Email:
r************@gmail.com

Posts by rbronste

<prev • 136 results • page 1 of 14 • next >
0
votes
2
answers
200
views
2
answers
Comment: C: BagFoot TF foot printing
... Yes Ive seen this one before however I think its more tuned towards DNase-seq data and I am working with ATAC-seq. ...
written 17 days ago by rbronste150
0
votes
1
answer
91
views
1
answers
Comment: C: DiffBind DESeq2 for multiple comparisons
... Right I know that part, but it is used within the framework of the DiffBind tool so that was more my question. ...
written 4 weeks ago by rbronste150
0
votes
1
answer
158
views
1
answers
Comment: C: tagAlign to BAM
... Thanks! So it processed it but with the following error: [bam_header_read] EOF marker is absent. The input is probably truncated. Wondering if it is critical to have that EOF marker? ...
written 4 weeks ago by rbronste150
1
vote
1
answer
158
views
1
answer
tagAlign to BAM
... Wondering if anyone knows how to convert the ENCODE generated tagAlign file (combo of several replicate BAMs) into a merged BAM file? Or is it necessary to take the individual replicate bam's and merge them separately? ...
encode bam tagalign written 4 weeks ago by rbronste150 • updated 4 weeks ago by venu4.5k
4
votes
2
answers
200
views
2
answers
BagFoot TF foot printing
... Wondering if anything has been able to successfully run this TF foot printing package outlined in the following paper? http://www.cell.com/cell-reports/fulltext/S2211-1247(17)30609-5 ...
R bagfoot bagfootr chip-seq written 4 weeks ago by rbronste150 • updated 18 days ago by simon.vanheeringen110
0
votes
0
answers
188
views
0
answers
Comment: C: Displaying/plotting numerous biological comparisons
... So I am not referring to the actual act of comparing, but rather taking many different conditions/their comparisons and displaying them clearly in a single graph of some sort. So for example different ages and treatments, all displayed together with a clear understanding of what I am comparing with ...
written 6 weeks ago by rbronste150
2
votes
0
answers
188
views
0
answers
Displaying/plotting numerous biological comparisons
... Wondering about a good way to visually represent/list many biological comparisons, was considering using an UpSetR plot but wanted to see what some other options are? Thanks. ...
plotting R written 6 weeks ago by rbronste150 • updated 7 days ago by Biostar ♦♦ 20
0
votes
1
answer
189
views
1
answers
Comment: C: Converting raw counts or DEseq2 output to TxDb container
... What would be your suggestion for how to best filter the GRanges object I get when I pull all transcripts from TxDb.Mmusculus.UCSC.mm10.knownGene against a DESeq output? Thanks again. ...
written 7 weeks ago by rbronste150
0
votes
1
answer
189
views
1
answers
Comment: C: Converting raw counts or DEseq2 output to TxDb container
... Thats exactly what I wanted to do, thanks! ...
written 7 weeks ago by rbronste150
0
votes
1
answer
189
views
1
answers
Comment: C: Converting raw counts or DEseq2 output to TxDb container
... So I am trying to limit the transcripts I run my ChIP-seq peaks against in the ChIPseeker package to those that are actually expressed in our system, instead of running the peaks and annotating against all transcripts. ...
written 8 weeks ago by rbronste150

Latest awards to rbronste

Centurion 3 months ago, created 100 posts.
Rising Star 6 months ago, created 50 posts within first three months of joining.
Supporter 6 months ago, voted at least 25 times.

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.3.0
Traffic: 1308 users visited in the last hour