User: benformatics

gravatar for benformatics
benformatics350
Reputation:
350
Status:
Trusted
Location:
Last seen:
6 hours ago
Joined:
2 years, 10 months ago
Email:
s*************@gmail.com

Posts by benformatics

<prev • 39 results • page 1 of 4 • next >
2
votes
1
answer
72
views
1
answers
Answer: A: Adding unique index or names to merged data frames
... Using the `plyr` package you can do the following: *Here the basic idea from cookbook-r.com:* # A sample factor to work with. x <- factor(c("alpha","beta","gamma","alpha","beta")) x #> [1] alpha beta gamma alpha beta #> Levels: alpha beta gamma levels(x) ...
written 13 days ago by benformatics350
0
votes
3
answers
172
views
3
answers
Answer: A: RNA-seq analysis using R
... You use limma after you have acquired your alignments (BAM files) and have generated a count table from them. Take a look a this guide for RNA-Seq: https://f1000research.com/articles/4-1070/v2 For a complete noob running your command line tools is not a simple task. I would recommend you get someo ...
written 13 days ago by benformatics350
0
votes
2
answers
130
views
2
answers
Comment: C: Evaluate overlap of regions
... you could also use sort() on that final object so that it is sorted ...
written 18 days ago by benformatics350
1
vote
2
answers
130
views
2
answers
Answer: A: Evaluate overlap of regions
... Given two GenomicRanges objects **a** and **b**. library(GenomicRanges) a <- GRanges("chr1:1000-1200") b <- GRanges("chr1:1100-1400") a$feature.1 <- 0.5 b$feature.1 <- 0.7 get.overlap.info <- function(a,b){ overlap.r <- intersect(a,b) dif ...
written 18 days ago by benformatics350
2
votes
2
answers
213
views
2
answers
Comment: C: smallRNA sequencing workflow and Database usage
... In regards to C) One thing to keep in mind is that piRNA are thought to be one of the most abundant class of small RNA in animals. As another user commented many of these annotations could actually be degradation products of other RNA or simply misclassification. On top of that there may even be ad ...
written 5 weeks ago by benformatics350
1
vote
0
answers
132
views
0
answers
Comment: C: Can anyone suggest me R code for Venndiagram?
... library(Vennerable) subset.1.names <- c('cat','dog','cow') subset.2.names <- c('bear','dog','fish') subset.3.names <- c('mouse','dog','fish') Vdf <- Venn(SetNames = c('one','two','three'),list(subset.1.names,subset.2.names,subset.3.names)) plot(Vdf, doW ...
written 6 weeks ago by benformatics350
1
vote
1
answer
141
views
1
answers
Answer: A: overlapping GRanges and GAlignments objects - "within" type results depend on "m
... Seems like a possible bug but also looks to be related to the classes used. If you convert the GAlignments object to GRanges, it works as expected. ## setting up your same objects genomic_region.gr <- GRanges("chrY:42301297-42301688:+") single_read.gal <- as(GRanges("chrY:42301566 ...
written 12 weeks ago by benformatics350
0
votes
2
answers
214
views
2
answers
Comment: C: Trying to add ensembl_transcript_id using Biomart
... **WARNING** Please be aware that you are **arbitrarily** adding a transcript_id to each of your genes. Each gene can have multiple transcripts associated it and in your case you are simply appending the *transcript_id* associated with the first occurrence of the *gene_id* in your biomaRt dataframe ...
written 12 weeks ago by benformatics350
1
vote
1
answer
243
views
1
answers
Comment: C: Macs called peaks shorter than 1kb
... All I'm trying to do is answer OP's question. If their data is spikey (as seems to be the case) then using narrowPeaks is not going to be ideal. Whether this spikey-ness is due to a bad MACS command, bad experimental protocol, or simply just sequencing artifacts, it is really hard to tell without mo ...
written 12 weeks ago by benformatics350
1
vote
1
answer
243
views
1
answers
Comment: C: Macs called peaks shorter than 1kb
... I beg to differ: > We used the gappedPeak representation for the histone marks with > relatively compact enrichment patterns. These include H3K4me3, > H3K4me2, H3K4me1, H3K9ac, H3K27ac and H2A.Z. ...
written 12 weeks ago by benformatics350

Latest awards to benformatics

Scholar 13 days ago, created an answer that has been accepted. For A: get mRNAs by TxDb
Teacher 8 weeks ago, created an answer with at least 3 up-votes. For A: ATAC-seq peak calling with MACS
Scholar 11 weeks ago, created an answer that has been accepted. For A: get mRNAs by TxDb
Scholar 12 weeks ago, created an answer that has been accepted. For A: get mRNAs by TxDb
Teacher 3 months ago, created an answer with at least 3 up-votes. For A: ATAC-seq peak calling with MACS
Teacher 3 months ago, created an answer with at least 3 up-votes. For A: ATAC-seq peak calling with MACS
Scholar 15 months ago, created an answer that has been accepted. For A: get mRNAs by TxDb
Appreciated 15 months ago, created a post with more than 5 votes. For A: ATAC-seq peak calling with MACS
Good Answer 15 months ago, created an answer that was upvoted at least 5 times. For A: ATAC-seq peak calling with MACS
Teacher 2.3 years ago, created an answer with at least 3 up-votes. For A: ATAC-seq peak calling with MACS

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.3.0
Traffic: 1539 users visited in the last hour