User: gundalav
gundalav • 300
- Reputation:
- 300
- Status:
- Trusted
- Location:
- La La Land
- Last seen:
- 5 months, 2 weeks ago
- Joined:
- 7 years, 6 months ago
- Email:
- g*******@gmail.com
about me
Posts by gundalav
<prev
• 51 results •
page 1 of 6 •
next >
0
votes
0
answers
141
views
0
answers
... I'm testing the [Monocle3][1] (version 0.2.0) with the following code. The main aim of this analysis is to identify differentially expressed genes for every time point.
library(monocle3)
library(dplyr) # imported for some downstream data manipulation
expression_matrix <- ...
written 5 months ago by
gundalav • 300
2
votes
1
answer
501
views
1
answer
... I have the following [GenomicRanges][1] object created with this:
library(GenomicRanges)
gr <- GRanges(seqnames = "chr1", strand = c("+", "-","-", "+"),ranges = IRanges(start = c(1,3,3,5), width = 3))
gr
That looks like this:
GRanges object with 4 ranges and 0 metadata columns ...
0
votes
1
answer
443
views
1
answer
... I have the following code:
library(Gviz)
library(Mus.musculus)
library(data.table)
library(OrganismDbi)
library(TxDb.Mmusculus.UCSC.mm10.knownGene)
txdb <- TxDb.Mmusculus.UCSC.mm10.knownGene
# Define bam file -----
adipose_bam <- "myfile.bam"
...
0
votes
2
answers
2.6k
views
2
answers
... Yes I have. BTW what I mean by RG tag is the one indicated in every read not as `@RG` header. ...
written 2.0 years ago by
gundalav • 300
6
votes
2
answers
2.6k
views
2
answers
... I have a BAM file that looks like this:
![enter image description here][1]
As you notice that the barcodes are included as part of read names.
Then I'm trying to use a [tool called chromVAR][2] that require `RG` tag to be included in the BAM file. RG tags are used to distinguish reads from diffe ...
written 2.0 years ago by
gundalav • 300
• updated
24 months ago by
finswimmer ♦ 13k
3
votes
1
answer
1.7k
views
1
answer
... I have the following two [GenomicRanges][1] objects. First one `gr1` is this:
library(GenomicRanges)
set.seed(1)
gr1 <- GRanges(
seqnames=Rle(c("chr1", "chr2", "chr1", "chr3"), c(1, 3, 2, 4)),
ranges=IRanges(1:10, width=10:1, names=head(letters,10)),
...
written 2.5 years ago by
gundalav • 300
• updated
2.5 years ago by
Sean Davis ♦ 26k
0
votes
1
answer
1.6k
views
1
answers
... @ATPoint Thanks for your reply. Speed is less of a concern at the moment, but rather the **correctness** of Method1. I tried using `cut -f1,2,6,7,8,9`. But the Method1 is totally uncorrelated (different) from Method2 and Method3. I need to be convinced why Method1 is incorrect. Your enlightenment wi ...
written 2.8 years ago by
gundalav • 300
4
votes
1
answer
1.6k
views
5 follow
1
answer
... I have the following BAM file and a annotation file.
The BAM is a paired end alignment.
What I want to do is to calculate reads (as fragment) count in
I can do it with the following three methods.
- **Method1:** [bedtools intersect][1]
- **Method2:** [bedtools multicov][2]
- **Method3:** [fea ...
written 2.8 years ago by
gundalav • 300
0
votes
2
answers
2.7k
views
2
answers
... Thanks. `airway@assays$data$counts` is that normalized or not? If not how can I get the normalized one from S4? ...
written 3.1 years ago by
gundalav • 300
11
votes
2
answers
2.7k
views
10 follow
2
answers
... I have the following DESeq2 code and the corresponding results
suppressMessages(library(DESeq2))
suppressMessages(library(airway))
data(airway)
airway_se <- airway
airway_dds <- DESeqDataSet(airway_se, design = ~cell + dex)
deseq <- DESeq(airway_dds)
#> ...
Latest awards to gundalav
Great Question
11 months ago,
created a question with more than 5,000 views.
For Creating Barplot With Horizontal Marker And Asterisks For Biological Paper
Epic Question
11 months ago,
created a question with more than 10,000 views.
For Creating Barplot With Horizontal Marker And Asterisks For Biological Paper
Popular Question
11 months ago,
created a question with more than 1,000 views.
For Non-Immune cell type gene expression database
Popular Question
16 months ago,
created a question with more than 1,000 views.
For Non-Immune cell type gene expression database
Popular Question
16 months ago,
created a question with more than 1,000 views.
For Mirna Disease Annotated Corpus
Popular Question
16 months ago,
created a question with more than 1,000 views.
For Visualizing Up/Down Regulation Of Genes Based On Fold Change
Popular Question
24 months ago,
created a question with more than 1,000 views.
For Non-Immune cell type gene expression database
Popular Question
24 months ago,
created a question with more than 1,000 views.
For Mirna Disease Annotated Corpus
Popular Question
24 months ago,
created a question with more than 1,000 views.
For Visualizing Up/Down Regulation Of Genes Based On Fold Change
Popular Question
24 months ago,
created a question with more than 1,000 views.
For Your Favorite Mirna-Gene Concordance Database Resource
Popular Question
24 months ago,
created a question with more than 1,000 views.
For Why mapping rate is low after adapter trimming paired-end data?
Popular Question
2.0 years ago,
created a question with more than 1,000 views.
For Non-Immune cell type gene expression database
Popular Question
2.0 years ago,
created a question with more than 1,000 views.
For Non-Immune cell type gene expression database
Popular Question
2.5 years ago,
created a question with more than 1,000 views.
For Non-Immune cell type gene expression database
Popular Question
2.7 years ago,
created a question with more than 1,000 views.
For Non-Immune cell type gene expression database
Popular Question
2.7 years ago,
created a question with more than 1,000 views.
For Visualizing Up/Down Regulation Of Genes Based On Fold Change
Popular Question
3.1 years ago,
created a question with more than 1,000 views.
For Visualizing Up/Down Regulation Of Genes Based On Fold Change
Epic Question
3.3 years ago,
created a question with more than 10,000 views.
For Creating Barplot With Horizontal Marker And Asterisks For Biological Paper
Popular Question
3.3 years ago,
created a question with more than 1,000 views.
For Best Way To Measure Mirna-Seq Abundance
Great Question
3.7 years ago,
created a question with more than 5,000 views.
For Creating Barplot With Horizontal Marker And Asterisks For Biological Paper
Popular Question
3.7 years ago,
created a question with more than 1,000 views.
For How To Make Cytoscape Export Network In Cluster Format (Non-Sif)
Great Question
5.0 years ago,
created a question with more than 5,000 views.
For Creating Barplot With Horizontal Marker And Asterisks For Biological Paper
Popular Question
5.0 years ago,
created a question with more than 1,000 views.
For How To Identify Tissue Specific Genes From Mixed Samples In Microarray Data
Popular Question
5.0 years ago,
created a question with more than 1,000 views.
For Best Way To Measure Mirna-Seq Abundance
Popular Question
5.0 years ago,
created a question with more than 1,000 views.
For How To Embed Ucsc Genome Browser To Web Page
Use of this site constitutes acceptance of our User
Agreement
and Privacy
Policy.
Powered by Biostar
version 2.3.0
Traffic: 1944 users visited in the last hour