3
votes
8
replies
973
views
0
votes
3
replies
448
views
0
votes
1
reply
293
views
4
votes
9
replies
790
views
2
votes
2
replies
301
views
updated 3 months ago by
Assa Yeroslaviz
★
1.9k
•
written 3 months ago by
gogeni5529
▴
50
2
votes
1
reply
322
views
updated 3 months ago by
dsull
★
6.9k
•
written 3 months ago by
biotrekker
▴
100
2
votes
2
replies
448
views
4
votes
3
replies
489
views
updated 3 months ago by
dsull
★
6.9k
•
written 3 months ago by
naili mortadha
•
0
2
votes
4
replies
467
views
4 months ago by
gogeni5529
▴
50
4
votes
2
replies
611
views
updated 4 months ago by
rfran010
★
1.3k
•
written 4 months ago by
Assa Yeroslaviz
★
1.9k
1
vote
2
replies
345
views
4 months ago by
Meghan.T
•
0
0
votes
6
replies
589
views
2
votes
2
replies
384
views
1
vote
3
replies
464
views
2
votes
2
replies
911
views
5 months ago by
Mohamed Abderrahmane
▴
20
2
votes
3
replies
541
views
1
vote
5
replies
1.0k
views
3
votes
2
replies
601
views
1
vote
2
replies
444
views
2
votes
6
replies
1.1k
views
0
votes
1
reply
376
views
updated 8 months ago by
dsull
★
6.9k
•
written 8 months ago by
Wintermute
•
0
3
votes
7
replies
904
views
1
vote
2
replies
587
views
0
votes
4
replies
586
views
updated 9 months ago by
i.sudbery
20k
•
written 9 months ago by
bsmith030465
▴
240
1
vote
3
replies
756
views
updated 10 months ago by
dsull
★
6.9k
•
written 10 months ago by
myoui3122010
▴
20
3
votes
3
replies
861
views
updated 10 months ago by
GenoMax
146k
•
written 10 months ago by
myoui3122010
▴
20
2
votes
5
replies
1.1k
views
2
votes
6
replies
1.1k
views
updated 11 months ago by
Brian Bushnell
20k
•
written 11 months ago by
Roberto
▴
20
3
votes
4
replies
927
views
3
votes
4
replies
1.3k
views
1
vote
4
replies
955
views
1
vote
5
replies
2.1k
views
6
votes
3
replies
827
views
updated 8 weeks ago by
binbinZhao
•
0
•
written 13 months ago by
butterman16
▴
30
0
votes
2
replies
625
views
3
votes
3
replies
867
views
7
votes
10
replies
2.0k
views
16 months ago by
firefox91
•
0
0
votes
1
reply
598
views
1
vote
0
replies
476
views
4
votes
5
replies
978
views
1
vote
7
replies
1.9k
views
0
votes
2
replies
993
views
1
vote
9
replies
2.7k
views
updated 18 months ago by
dsull
★
6.9k
•
written 18 months ago by
micecanfly
▴
10
0
votes
1
reply
496
views
1
vote
6
replies
1.2k
views
1
vote
2
replies
940
views
updated 16 months ago by
Ram
44k
•
written 19 months ago by
tritone_858
•
0
7
votes
5
replies
1.2k
views
6
votes
4
replies
2.5k
views
1
vote
1
reply
688
views
8
votes
13
replies
2.1k
views
20 months ago by
txema.heredia
▴
190
3
votes
2
replies
658
views
Recent Votes
Recent Locations •
All
Frankrike, 1 minute ago
France/Nantes/Institut du Thorax - INSERM UMR1087, 5 minutes ago
United States, 8 minutes ago
UCLA, 10 minutes ago
France, 14 minutes ago
Bologna, 16 minutes ago
EMBL Heidelberg, Germany, 19 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: 992 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