User: cguzman.roma

gravatar for cguzman.roma
Reputation:
0
Status:
New User
Last seen:
2 years, 7 months ago
Joined:
4 years ago
Email:
c***********@gmail.com

Profile information, website and location are not shown for new users.

This helps us discourage the inappropriate use of our site.

Posts by cguzman.roma

<prev • 8 results • page 1 of 1 • next >
0
votes
1
answer
950
views
1
answers
Comment: C: How to determine a set of empirical control 'genes' using RUVSeq
... This is sort of what I expected. Definetely not all repeats are influenced by the KO, and I do have access to KO gene expression RNA-seq data, I could potentially look at that. ...
written 2.6 years ago by cguzman.roma0
2
votes
1
answer
950
views
1
answer
How to determine a set of empirical control 'genes' using RUVSeq
... I'm attempting to identify differentially expressed repeats (in this case those of the LTR family) in human genome 38. The data I am working with is 4sU-seq data, which essentially captures RNAs that are produced within a 10 minute time period. The data however, contains many intronic and exonic rea ...
ruvseq written 2.6 years ago by cguzman.roma0
0
votes
2
answers
577
views
2
answers
annotatr GRanges Error
... Am receiving this error and not sure how to continue. I am trying to annotate my ChIP-seq peaks to various loci and am using the 'annotatr' package. Workflow: library(annotatr) data <- read_regions(con = "TRIM28_MACS2.broadPeak.forR.bed", genome = 'hg38', format = 'bed') ...
annotatr written 2.7 years ago by cguzman.roma0 • updated 2.7 years ago by rcavalca130
1
vote
0
answers
1.1k
views
0
answers
clusterProfiler - enrichGO and enrichPathway not returning any results
... I'm attempting to run some gene ontology analysis as well as pathway analysis using the Reactome database, but i'm running into something interesting. I'm not returning any results. So whenever I go to visualize my data using a dotplot, it returns an empty image. What am I doing wrong? File is a 6 ...
clusterprofiler written 2.7 years ago by cguzman.roma0
0
votes
1
answer
987
views
1
answers
Comment: C: ChIPseeker: Is it possible to create heatmaps / metagene plots without being cen
... When you say "I can modify it to intron or exon level" you mean .. you as the developer and then push out an update that would allow us to do this or this is something I can accomplish at this moment too? Probably a silly question but oh well.   Thanks a ton, ...
written 4.0 years ago by cguzman.roma0
0
votes
1
answer
788
views
1
answers
Comment: C: ChIPseeker Error: Attempting to annotatePeaks
... 1. Thank you, am looking forward to this. It is also possible add a by="intron" as well? I'm not sure how much more difficult this would be. This would greatly reduce the headaches for my current research. 2. Fixed. Thank you! ...
written 4.0 years ago by cguzman.roma0
1
vote
1
answer
987
views
1
answer
ChIPseeker: Is it possible to create heatmaps / metagene plots without being centered on the TSS?
... So if you look at https://bioconductor.riken.jp/packages/3.2/bioc/vignettes/ChIPseeker/inst/doc/ChIPseeker.html you will notice that most of the data generated is centered on the TSS.    I would like to know if it is possible to center metagene plots (and other data) either at the start of exons / ...
chipseq chipseeker exon start site written 4.0 years ago by cguzman.roma0 • updated 4.0 years ago by Guangchuang Yu1.1k
1
vote
1
answer
788
views
1
answer
ChIPseeker Error: Attempting to annotatePeaks
... Hello everyone, I am attempting to annotate some ChIP-Seq data that I have called using MACS2. The output of MACS2 is .narrowPeak format. I was able to successfully convert my ChIP Seq data to GRanges using: peakstoanno = readPeakFile(file.path("/home/carlos/data/Sample_Pol-II-Chip/Peaks/narrow/P ...
chipseeker software error written 4.0 years ago by cguzman.roma0 • updated 4.0 years ago by Guangchuang Yu1.1k

Latest awards to cguzman.roma

No awards yet. Soon to come :-)

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 16.09
Traffic: 215 users visited in the last hour