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recount3
•
reset
8
votes
8
replies
251
views
Counts from recount3 for DESeq2 analysis
recount3
DESeq2
5 weeks ago
william.benit
▴ 10
0
votes
2
replies
142
views
Missing sample in recount3 data
recount3
9 weeks ago • updated 27 days ago
alex.dietrich
• 0
0
votes
1
reply
124
views
Retrieve the read counts per transcript instead of per gene
recount3
updated 7 weeks ago by
Leonardo Collado Torres
▴ 980 • written 9 weeks ago by
oligoelemento
▴ 10
11
votes
8
replies
830
views
Error when downloading data with recount3.
recount3
updated 7 weeks ago by
chris.wilks
▴ 40 • written 19 months ago by
Zach Brehm
▴ 20
1
vote
1
reply
159
views
recount3 - download bigwig files for TCGA data
recount3
recount
TCGA
updated 8 weeks ago by
Leonardo Collado Torres
▴ 980 • written 8 weeks ago by
Xuebing
▴ 10
0
votes
1
reply
132
views
Sample tissue annotation
recount3
updated 12 weeks ago by
Leonardo Collado Torres
▴ 980 • written 3 months ago by
M.M.M.M.
• 0
0
votes
1
reply
219
views
Distinguishing between single cell and bulk data in recount3 study explorer
recount3
updated 12 weeks ago by
Leonardo Collado Torres
▴ 980 • written 5 months ago by
kstachelek
• 0
0
votes
2
replies
334
views
Get read counts for TCGA samples via recount3
recount3
6 months ago
mario.keller.1988
▴ 10
2
votes
2
replies
265
views
[recount3] Merge gene counts tables from multiple projects (SRP)
recount3
recountWorkflow
updated 7 months ago by
Leonardo Collado Torres
▴ 980 • written 7 months ago by
António Miguel de Jesus Domingues
▴ 480
0
votes
1
reply
193
views
Different read support for splice junctions using snapcount and recount3
recount3
snapcount
updated 7 months ago by
Leonardo Collado Torres
▴ 980 • written 7 months ago by
mario.keller.1988
▴ 10
2
votes
3
replies
363
views
Downloading count matrix for full recount3 dataset
recount3
10 months ago
Ben
• 0
0
votes
2
replies
416
views
recount3: advice for working with an unannotated genes
recount3
updated 6 months ago by
devorah.fialkoff
• 0 • written 12 months ago by
MakeTheBrain
• 0
1
vote
1
reply
413
views
Correlation analyses on TCGA data
RNA-seq
Normalization
edgeR
recount3
updated 11 months ago by
Leonardo Collado Torres
▴ 980 • written 12 months ago by
mario.keller.1988
▴ 10
0
votes
1
reply
492
views
Using recount data to calculate Intron retention
snapcount
recount3
recount
updated 14 months ago by
Leonardo Collado Torres
▴ 980 • written 14 months ago by
Mariela Cortés López
• 0
14 results • Page
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Replies
Comment: CPM after RUVseq
by
James W. MacDonald
59k
Also, you might be confused about something. CPM is counts/million counts, which *uses library size to scale normalize* and logCPM is just…
Comment: CPM after RUVseq
by
James W. MacDonald
59k
You shouldn't use CPM or logCPM for any of the steps! To use `RUVr` you need to fit a preliminary model using `edgeR`, which takes counts a…
Comment: CPM after RUVseq
by
Jess
• 0
Thank you James! It hadn't occurred to me to input CPM rather than logCPM which is why my df$NormalizedCounts didn't exceed 17ish in valu…
Answer: RPX PXDataset error
by
Laurent Gatto
1.5k
- From the URL in the error, it looks like you have the latest (or a recent) `rpx` version. It is generally recommended to add the output o…
Answer: Package name already exists due to previous issue
by
shepherl
3.1k
This has been resolved. There needed to be a manual intervention by the core team to remove the old issue from the issue tracker database.…
Votes
Answer: CPM after RUVseq
Comment: Merging two plated in R
Answer: Merging two plated in R
Answer: Merging two plated in R
A: Can we use glmQLFit instead of glmFit and then glmLRT in edgeR
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