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18 results • Page
1 of 1
Sort: Rank
Rank
Views
Votes
Replies
0
votes
0
replies
25
views
How to assign cell types after integration in scRNA
integration
conditions
ScRNA
seq
2 hours ago by
Francesco
▴ 10
0
votes
0
replies
24
views
STAR total splices (in Log.final) vs collapsed splice junctions (in SJ.out.tab)
STAR
2 hours ago by
tnminh89
▴ 10
6
votes
6
replies
295
views
NGS forensics: how to know if data is fabricated
fastq
STAR
NGS
Illumina
updated 1 hour ago by
dsull
★ 5.9k • written 4 hours ago by
noodle
▴ 520
0
votes
0
replies
30
views
Extract protein sequence
fasta
alighment
blast
3 hours ago by
anna
▴ 20
0
votes
0
replies
38
views
Filter low express genes in microarray data
microarray
4 hours ago by
Chris
▴ 260
0
votes
1
reply
229
views
absolute path for symbolic links in Snakefile
Snakemake
updated 4 hours ago by
Jesse
▴ 740 • written 8 days ago by
yifangt86
▴ 60
0
votes
2
replies
226
views
Hide positions in alignment with 99% "–" characters to ignore single sequence insertions?
alignment
gaps
updated 4 hours ago by
Jesse
▴ 740 • written 2 days ago by
Broccoli
• 0
2
votes
3
replies
211
views
Source other conda environments in a nextflow pipeline when nextflow itself is in a conda environment?
hpc
conda
nextflow
updated 5 hours ago by
Arup Ghosh
3.2k • written 1 day ago by
chaco001
▴ 40
0
votes
2
replies
165
views
Help understanding how KEGG Ortholog `K00004 ` has 3 ECs associated with it (EC:1.1.1.4, 1.1.1.-, 1.1.1.303)?
ontology
metagenomics
database
enzymes
genomics
7 hours ago by
O.rka
▴ 710
0
votes
1
reply
132
views
Limma Analysis Agilent Microarray Data (GPL1708)
Microarray
Limma
Agilent
updated 20 hours ago by
Gordon Smyth
★ 7.0k • written 1 day ago by
hagl
▴ 10
0
votes
2
replies
165
views
Correct way to compare multiple treaments between RNA-Seq samples using edgeR?
RNA-Seq
edgeR
13 hours ago by
Guille
• 0
4
votes
8
replies
497
views
Create a new bed file with all pairwise combinations between two other bed files, based on bp distance
SNPs
BED
eqtl
bedtools
updated 19 hours ago by
Alex Reynolds
35k • written 1 day ago by
J
▴ 10
4
votes
7
replies
554
views
7 follow
Heatmap and rna-seq
RNA-Seq
Heatmap
updated 17 hours ago by
dsull
★ 5.9k • written 4 days ago by
qudrat.nii
▴ 10
1
vote
3
replies
197
views
gvcf joint calling
WES
GATK
VCF
gVCF
updated 7 hours ago by
Jeremy Leipzig
22k • written 1 day ago by
zihanss
• 0
1
vote
2
replies
206
views
ScRNAseq-How to correctly choose cell type marker genes
cellAssign
cell-markers
2 hours ago by
Francesco
▴ 10
1
vote
6
replies
344
views
ScRNA data question
scRNA
Vlnplot
Samples
12 hours ago by
starswillfade
▴ 10
4
votes
4
replies
370
views
Tutorial:
how to combine multiple RNAseq count files into a single dataframe in R and unix
Unix
RNAseq
R
updated 9 hours ago by
BioinfGuru
★ 1.7k • written 2 days ago by
Ming Tommy Tang
★ 3.9k
0
votes
5
replies
300
views
different FeatureCounts output for the same data
fpkm
Counts
Rsubread
rna-seq
updated 8 hours ago by
Istvan Albert
100k • written 3 days ago by
sehriban.buyukkilic
▴ 10
18 results • Page
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Comment: calculate nucleotide diversity from whole-genome-sequence data for individual ge
Comment: calculate nucleotide diversity from whole-genome-sequence data for individual ge
Answer: DNA methylation preprocessing
Comment: NGS forensics: how to know if data is fabricated
Answer: NGS forensics: how to know if data is fabricated
Comment: NGS forensics: how to know if data is fabricated
correcting for a batch in DESeq2
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Recent Replies
Comment: NGS forensics: how to know if data is fabricated
by
dsull
★ 5.9k
I don't think people have undertaken the effort to create an anomaly detector for RNAseq -- people's efforts are dedicated towards developi…
Comment: NGS forensics: how to know if data is fabricated
by
dsull
★ 5.9k
I'd say post on pubpeer -- it's the best forum for this sort of discussion. As for what additional analysis I recommend: I'd say look at s…
Comment: NGS forensics: how to know if data is fabricated
by
noodle
▴ 520
> This is a super-interesting question from an algorithmic standpoint Ya, I was hoping to find some algorithm that would compare say a 're…
Comment: ScRNAseq-How to correctly choose cell type marker genes
by
Francesco
▴ 10
Thank you for your valuable suggestion!
Comment: NGS forensics: how to know if data is fabricated
by
noodle
▴ 520
> My first question would be how strong your background in such analysis > is. Very strong. PhD+several years working in the field. > Wot…
Comment: NGS forensics: how to know if data is fabricated
by
ATpoint
82k
My first question would be how strong your background in such analysis is. Claim of fabrication is very serious, so be 100% sure to back it…
Answer: NGS forensics: how to know if data is fabricated
by
Jeremy Leipzig
22k
This is a super-interesting question from an algorithmic standpoint (devising a model that can distinguish real from synthetic reads) but I…
Answer: absolute path for symbolic links in Snakefile
by
Jesse
▴ 740
It's nothing to do with Snakemake, just the ordinary confusion of making relative symlinks when your working directory is somewhere else. …
Answer: Hide positions in alignment with 99% "–" characters to ignore single sequence in
by
Jesse
▴ 740
[seqmagick](https://github.com/fhcrc/seqmagick/) has a `--squeeze-threshold` option that does just this. For example with an MSA of five s…
Comment: Source other conda environments in a nextflow pipeline when nextflow itself is i
by
Arup Ghosh
3.2k
Use the standalone version of Nextflow and specify the process-specific conda environments paths.
Comment: gvcf joint calling
by
Jeremy Leipzig
22k
can you show us an exonic position in your VCF file that is all `./.`?
Comment: Help understanding how KEGG Ortholog `K00004 ` has 3 ECs associated with it (EC:
by
O.rka
▴ 710
Thank you. This answers my question. The reason I am asking is because I’m trying to do set enrichment analysis with BRENDA pathways using…
Answer: Source other conda environments in a nextflow pipeline when nextflow itself is i
by
colindaven
6.4k
I used to use nextflow in a conda env. That requires the env to be active when a pipeline is started. Also I have productive pipelines whic…
Comment: different FeatureCounts output for the same data
by
Istvan Albert
100k
just to clarify, it is not that the program algorithm works differently but the meaning of the flags changed; before -p was sufficient to…
Comment: how to combine multiple RNAseq count files into a single dataframe in R and unix
by
BioinfGuru
★ 1.7k
Thanks Ram. Using merge maxed out my ram on a large list, but your suggestion directed me to purrr::reduce which works great.
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