25 days ago by
buffealo
▴
130
5
votes
8
replies
689
views
0
votes
0
replies
146
views
0
votes
0
replies
175
views
0
votes
1
reply
282
views
updated 4 months ago by
Jack Tierney
▴
410
•
written 4 months ago by
Jaskaran Singh
•
0
3
votes
4
replies
607
views
4 months ago by
Jaskaran Singh
•
0
4
votes
2
replies
453
views
0
votes
1
reply
330
views
1
vote
2
replies
507
views
2
votes
2
replies
830
views
2
votes
4
replies
870
views
1
vote
0
replies
409
views
17 months ago by
Dan
▴
180
2
votes
3
replies
1.1k
views
updated 17 months ago by
rfran010
★
1.3k
•
written 17 months ago by
weimichelles
•
0
3
votes
6
replies
903
views
0
votes
0
replies
476
views
18 months ago by
bioinformatics.girl
▴
20
1
vote
1
reply
758
views
updated 18 months ago by
Rory Stark
★
2.1k
•
written 18 months ago by
Chris
▴
340
0
votes
2
replies
592
views
0
votes
0
replies
378
views
19 months ago by
weimichelles
•
0
1
vote
2
replies
3.3k
views
0
votes
1
reply
1.2k
views
updated 22 months ago by
Pierre Lindenbaum
164k
•
written 22 months ago by
bioinformatics.girl
▴
20
0
votes
2
replies
843
views
23 months ago by
bioinformatics.girl
▴
20
1
vote
4
replies
1.1k
views
5
votes
5
replies
1.9k
views
0
votes
1
reply
777
views
updated 2.2 years ago by
Friederike
9.0k
•
written 2.2 years ago by
rekharichardson
•
0
3
votes
3
replies
3.1k
views
4
votes
1
reply
630
views
0
votes
1
reply
978
views
updated 2.4 years ago by
bioinformatics.girl
▴
20
•
written 2.4 years ago by
francesca3
▴
150
2
votes
2
replies
1.5k
views
2
votes
9
replies
3.3k
views
4
votes
0
replies
927
views
0
votes
0
replies
403
views
0
votes
0
replies
631
views
0
votes
0
replies
378
views
3
votes
4
replies
3.1k
views
1
vote
1
reply
974
views
updated 2.8 years ago by
angadmaurya311
▴
10
•
written 2.8 years ago by
zq
•
0
7
votes
7
replies
4.4k
views
updated 7 months ago by
sgv
•
0
•
written 2.8 years ago by
sir.outman
▴
40
3
votes
5
replies
1.9k
views
1
vote
1
reply
1.7k
views
2
votes
2
replies
1.0k
views
3.0 years ago by
maxrwjones
▴
60
0
votes
5
replies
3.5k
views
0
votes
0
replies
673
views
3.2 years ago by
ahmad mousavi
▴
800
3
votes
2
replies
1.3k
views
1
vote
0
replies
579
views
0
votes
0
replies
554
views
3.2 years ago by
shangguandong1996
▴
30
0
votes
0
replies
462
views
3.2 years ago by
kvshamsudheen
▴
120
0
votes
2
replies
1.3k
views
2
votes
5
replies
1.3k
views
updated 3.4 years ago by
Lila M
★
1.3k
•
written 3.4 years ago by
shangguandong1996
▴
30
0
votes
5
replies
1.4k
views
1
vote
1
reply
959
views
updated 3.5 years ago by
heskett
▴
110
•
written 3.5 years ago by
ahmad mousavi
▴
800
0
votes
0
replies
1.3k
views
3.6 years ago by
ahmad mousavi
▴
800
0
votes
8
replies
2.4k
views
3.6 years ago by
abiuma
▴
30
Recent Votes
Recent Locations •
All
UCLA, just now
France, 4 minutes ago
Bologna, 6 minutes ago
EMBL Heidelberg, Germany, 9 minutes ago
Moscow, 9 minutes ago
United States, 13 minutes ago
Sheffield, UK, 18 minutes ago
Recent Awards •
All
Popular Question to
Charles Murtaugh
▴
50
Scholar to
Istvan Albert
101k
Popular Question to
Aki
▴
20
Popular Question to
from the mountains
▴
250
Popular Question to
Elisabeth Gasteiger
★
2.4k
Popular Question to
tyasird
▴
10
Recent Replies
Comment: Are there any preferred trajectory/pseudotime analyses that do not require an ar
by
Jean-Karim Heriche
27k
Maybe consider seriation/ordination as an alternative.
Comment: dedup STAR transcriptome file using umi_tools
by
i.sudbery
20k
There are bulk protocols that include UMIs. Lexogen's CORRAL kits for example. Or NEB's NEBNext UMI adaptors.
Answer: dedup STAR transcriptome file using umi_tools
by
Michael
55k
I am quite sure that you cannot use UMI_tools to deduplicate bulk RNA-seq. The different oligo adapter sequences on each bead introduce UMI…
Answer: dedup STAR transcriptome file using umi_tools
by
i.sudbery
20k
I don't know if any reason you shouldn't be able to index the bam produced by STAR, although you will need to sort them first.
Comment: Compare Two Sigle-cell Sample for Differentially Expressed Genes (DEGs). How?
by
wangziwei0010
▴
30
Hi ATpoint,
Thank you for your though provoking answer. Big fans!
Actually I have some normal cells in each sample, and I found good mixt…
Answer: Differential binding analysis between different TFs
by
Ming Tommy Tang
★
4.5k
have you taken a look at csaw? https://bioconductor.org/books/release/csawBook/
also, I am not sure how you can compare different TFs, the…
Comment: R encountering fatal error and quitting the session
by
Dunois
★
2.7k
Have you tried running this in a fresh, clean `R` session with no other (unnecessary) packages and data being loaded into memory? How much …
Comment: PyDeseq2 - InvalidIndexError
by
Dunois
★
2.7k
You most likely have duplicates somewhere in there in the column that is currently serving as index to (I am guessing) the counts DataFrmae…
Comment: What to do with sequences without hits after doing blast against a reference tra
by
Dunois
★
2.7k
Expand your search by searching these (two) sequences against other sets of sequences.
That said, why does it feel like this is an [XY pro…
Comment: Compare Two Sigle-cell Sample for Differentially Expressed Genes (DEGs). How?
by
ATpoint
85k
It's confounded. SCtransform is not doing anything in such situations and hatmony operates on a per-cell embeddings level and not per gene …
Comment: count number of polymorphic sites among samples in vcf
by
vaellis
•
0
I'm wondering if this could work:
`bcftools query -f '[%GT]\n' my.vcf.gz | awk '{ gsub(/\./, ""); print }' | grep -Ev '^(.)\1+$' | wc -l`
…
Comment: GISTIC 2.0 parameter change not happening
by
Ram
44k
You should contact the [GenePattern google group](https://groups.google.com/g/genepattern-help) - that's where you stand a higher chance of…
Comment: find marker using scRNAseq data
by
allingt
•
0
What method are you using to identify markers and does it allow for nested designs?
Comment: count number of polymorphic sites among samples in vcf
by
vaellis
•
0
I will look into this. Thank you!
Comment: count number of polymorphic sites among samples in vcf
by
vaellis
•
0
example vcf:
```
CHROM POS ID REF ALT QUAL FILTER INFO FORMAT ind1 ind2 ind3 ind4
chr1 100 . C …
Traffic: 976 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