5
votes
3
replies
231
views
0
votes
0
replies
162
views
4
votes
2
replies
283
views
7
votes
7
replies
1.2k
views
updated 11 days ago by
Dunois
★
2.5k
•
written 11 days ago by
AdviceSeeker
•
0
1
vote
2
replies
339
views
16
votes
10
replies
1.0k
views
6 follow
updated 28 days ago by
Madelaine Gogol
5.3k
•
written 29 days ago by
Ann
★
2.4k
103
votes
42
replies
31k
views
34 follow
updated 18 days ago by
Jeremy Leipzig
22k
•
written 10.5 years ago by
14134125465346445
★
3.6k
25
votes
11
replies
3.7k
views
6 follow
Forum:
Site Use Guidelines
updated 3 days ago by
Ram
43k
•
written 14.6 years ago by
Istvan Albert
100k
Recent Votes
Recent Locations •
All
United States, 1 minute ago
Belgium, 3 minutes ago
Canada, 3 minutes ago
United States, 4 minutes ago
United States, 5 minutes ago
France, 6 minutes ago
United States, 8 minutes ago
Recent Awards •
All
Popular Question to
chaco001
▴
40
Commentator to
GenoMax
141k
Popular Question to
rheab1230
▴
140
Popular Question to
BioinfGuru
★
1.7k
Popular Question to
vinayjrao
▴
250
Supporter to
Jalil Sharif
▴
80
Recent Replies
Comment: Create a new bed file with all pairwise combinations between two other bed files
by
J
•
0
Thank you Pierre! I'll try this out with my full data set.
Answer: DNA methylation preprocessing
by
cao510927
▴
30
I happend to see one paper doing the similar thing, share it with you guys, "A systematic evaluation of normalization methods and probe rep…
Answer: Create a new bed file with all pairwise combinations between two other bed files
by
Alex Reynolds
35k
I think Pierre's answer might be correct for your test input, but it doesn't account for the start position of the reference element and so…
Comment: Highest variable features in single cell data
by
bk11
★
2.4k
You need to be clear about how `Seurat` defines highly variable genes here. Highly variable genes are the genes that have very high express…
Comment: Heatmap and rna-seq
by
GenoMax
141k
Please include a link when you are recommending a tool. There can be programs with similar names.
Comment: how to combine multiple RNAseq count files into a single dataframe in R and unix
by
Ram
43k
Simple:
```r
data <- lapply(files, read_tsv)
data <- Reduce(merge, data) # or Reduce(full_join, data)
```
<a href="" title="Text added bec…
Answer: Source other conda environments in a nextflow pipeline when nextflow itself is i
by
ATpoint
82k
You can make each process use a dedicated environment, see https://www.nextflow.io/docs/latest/conda.html#use-existing-conda-environments
…
Comment: how to combine multiple RNAseq count files into a single dataframe in R and unix
by
BioinfGuru
★
1.7k
Hi,
Just thought I'd share this code snippet here for when each file contains multiple samples. I tried using lapply (as suggested by Ram)…
Comment: Low mapping rate with Salmon
by
i.sudbery
19k
Take your STAR alignment and sum all the counts for each gene. You can either do this by providing an annotation to STAR, or by running fea…
Comment: How to convert plink files to Hapmap Format
by
bk11
★
2.4k
If you run your data with plink 2.0, you will have ERRCODE column in your result file showing the reason behind "NA" p-value.
https://www.b…
Comment: genome assembly records not present in assembly_summary.txt
by
sapuizait
▴
10
jesus its in the Genbank file and I was looking at the refseq! I m such a moron - thanks for pointing it out -sorry about that :(
Comment: ScRNA data question
by
bk11
★
2.4k
I wonder how the `Vlnplots` will look if you normalize the data using `NormalizeData()` function in `Seurat`. The flat line in your plot ar…
Comment: Low mapping rate with Salmon
by
GenoMax
141k
> Does that mean that the reads that are not mapped to my trascriptome are not exons/coding genes?
Reads are likely aligning in regions wh…
Comment: How Can We Find The Info For 3'Utr And 5'Utr In Gencode Gtf File?
by
cmdcolin
★
3.8k
the gencode link is broken now but here is a back up of that blogpost on archive https://web.archive.org/web/20130618221342/http://gencodeg…
Traffic: 2330 users visited in the last hour
Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by the
version 2.3.6
version 2.3.6