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Showing :
recount3
•
reset
0
votes
0
replies
165
views
Recount3 error downloading data
recount3
recount
11 weeks ago
Max Bone
• 0
1
vote
1
reply
196
views
Transcript level expression for CCLE
recount3
recount
CCLE
updated 12 weeks ago by
Leonardo Collado Torres
★ 1.0k • written 12 weeks ago by
António Miguel de Jesus Domingues
▴ 490
0
votes
2
replies
519
views
TCGA counts to TPM from recount3 do not seem to right
recount3
TCGA
RNASeq
updated 5 months ago by
Leonardo Collado Torres
★ 1.0k • written 6 months ago by
tangming2005
▴ 190
0
votes
2
replies
509
views
recount3 monorail pipeline version
recount3
6 months ago • updated 4 months ago
Lorenzo
• 0
0
votes
2
replies
490
views
Recount3: PCR duplicates
pcrduplicates
recount3
multimappingreads
updated 10 months ago by
ivanrebecca230
• 0 • written 11 months ago by
seline.natalie
• 0
0
votes
3
replies
1.5k
views
Recount3 error with default "recount3_url" option
recount3
updated 11 months ago by
Leonardo Collado Torres
★ 1.0k • written 17 months ago by
Cornwell, Adam
▴ 110
0
votes
2
replies
785
views
Recount3 data download problem
recount
recount3
updated 11 months ago by
Leonardo Collado Torres
★ 1.0k • written 16 months ago by
franceschini.gianmarco
• 0
2
votes
6
replies
1.3k
views
Unable to load data from duffel.rail
recount
recountWorkflow
recount3
updated 11 months ago by
Leonardo Collado Torres
★ 1.0k • written 16 months ago by
Max Bone
• 0
2
votes
11
replies
1.5k
views
Not able to download recount3 data
recount3
updated 11 months ago by
Leonardo Collado Torres
★ 1.0k • written 16 months ago by
Niveditha
▴ 20
0
votes
2
replies
676
views
Cannot download data from IDIES links
recount
recountWorkflow
recount3
updated 11 months ago by
Leonardo Collado Torres
★ 1.0k • written 16 months ago by
dml
• 0
1
vote
3
replies
998
views
Can i perform DEseq2 from 2 different rse objects download from RECOUNT database
DESeq2
recount
GTEx
TCGA
recount3
updated 11 months ago by
ATpoint
★ 4.0k • written 11 months ago by
David
▴ 20
0
votes
1
reply
555
views
Recount3 data correspond to TCGA data
recount3
updated 10 months ago by
seline.natalie
• 0 • written 12 months ago by
kevin lee
• 0
2
votes
3
replies
753
views
BigWig files provided by recount3
recount3
updated 13 months ago by
Leonardo Collado Torres
★ 1.0k • written 13 months ago by
mario.keller.1988
▴ 20
4
votes
6
replies
918
views
recount 3 protect read length metadata
recountWorkflow
recount3
updated 15 months ago by
Leonardo Collado Torres
★ 1.0k • written 16 months ago by
soever
▴ 20
1
vote
1
reply
723
views
searching study metadata in recount3
recount3
updated 18 months ago by
Leonardo Collado Torres
★ 1.0k • written 18 months ago by
andrew.su
▴ 10
0
votes
1
reply
697
views
recount3 transform_counts vs compute_read_counts
recount3
updated 20 months ago by
Leonardo Collado Torres
★ 1.0k • written 20 months ago by
fdelillo
• 0
2
votes
2
replies
1.9k
views
Create TPM gene tables/dataframe from ReCount3
recount3
TCGA
GTEx
DESeq2
22 months ago
David
▴ 20
10
votes
11
replies
2.3k
views
Counts from recount3 for DESeq2 analysis
recount3
DESeq2
updated 20 months ago by
Leonardo Collado Torres
★ 1.0k • written 2.0 years ago by
william.benit
▴ 10
0
votes
2
replies
882
views
Missing sample in recount3 data
recount3
2.1 years ago • updated 24 months ago
alex.dietrich
• 0
0
votes
1
reply
849
views
Retrieve the read counts per transcript instead of per gene
recount3
updated 2.1 years ago by
Leonardo Collado Torres
★ 1.0k • written 2.1 years ago by
oligoelemento
▴ 10
11
votes
8
replies
2.1k
views
Error when downloading data with recount3.
recount3
updated 2.1 years ago by
chris.wilks
▴ 70 • written 3.5 years ago by
Zach Brehm
▴ 20
1
vote
1
reply
1.1k
views
recount3 - download bigwig files for TCGA data
recount3
recount
TCGA
updated 2.1 years ago by
Leonardo Collado Torres
★ 1.0k • written 2.1 years ago by
Xuebing
▴ 10
0
votes
1
reply
640
views
Sample tissue annotation
recount3
updated 2.1 years ago by
Leonardo Collado Torres
★ 1.0k • written 2.2 years ago by
M.M.M.M.
• 0
0
votes
1
reply
836
views
Distinguishing between single cell and bulk data in recount3 study explorer
recount3
updated 2.1 years ago by
Leonardo Collado Torres
★ 1.0k • written 2.4 years ago by
kstachelek
• 0
0
votes
2
replies
1.5k
views
Get read counts for TCGA samples via recount3
recount3
2.5 years ago • updated 2.4 years ago
mario.keller.1988
▴ 20
2
votes
2
replies
1.1k
views
[recount3] Merge gene counts tables from multiple projects (SRP)
recount3
recountWorkflow
updated 2.5 years ago by
Leonardo Collado Torres
★ 1.0k • written 2.6 years ago by
António Miguel de Jesus Domingues
▴ 490
0
votes
1
reply
781
views
Different read support for splice junctions using snapcount and recount3
recount3
snapcount
updated 2.5 years ago by
Leonardo Collado Torres
★ 1.0k • written 2.5 years ago by
mario.keller.1988
▴ 20
2
votes
5
replies
1.3k
views
Downloading count matrix for full recount3 dataset
recount3
updated 5 weeks ago by
Leonardo Collado Torres
★ 1.0k • written 2.8 years ago by
Ben
• 0
0
votes
2
replies
1.1k
views
recount3: advice for working with an unannotated genes
recount3
updated 2.4 years ago by
devorah.fialkoff
• 0 • written 2.9 years ago by
MakeTheBrain
• 0
1
vote
1
reply
1.7k
views
Correlation analyses on TCGA data
RNA-seq
Normalization
edgeR
recount3
updated 2.9 years ago by
Leonardo Collado Torres
★ 1.0k • written 2.9 years ago by
mario.keller.1988
▴ 20
0
votes
1
reply
1.2k
views
Using recount data to calculate Intron retention
snapcount
recount3
recount
updated 3.1 years ago by
Leonardo Collado Torres
★ 1.0k • written 3.1 years ago by
Mariela Cortés López
• 0
31 results • Page
1 of 1
Recent ...
Replies
Answer: DESEQ2 IHW and Apelgm method for Shrinkage (adding s values to FDR)
by
Michael Love
41k
> I got many p values that had "1.000000e+00" and padj "1" and stat of "0" when I added the Log threshold of LFC >1 and LFC < -1...is this …
Comment: Trying to use enrichGO
by
fernanda.backsouza
▴ 10
With all my love, thank you Guido, GOxploreR beeing a big ally for me. I don't know how to be grateful right now.
Comment: DESeq2 output used for PCA plot on R studio
by
swbarnes2
★ 1.3k
You didn't generate it with an experiment, you made it up: Your PCA doesn't look like a good RNASeq experiment, because it's not.
Answer: Opposite sign of LFC in count plots of DEGs (DESeq2)
by
swbarnes2
★ 1.3k
Your contrast is comparing LGR5 to Homeostasis. The bottom 2 are fine, it's the top one that is wrong. Are you sure this step isn't misla…
Comment: get BM error
by
James W. MacDonald
65k
I believe you need NCBI Gene IDs for KEGG, in which case you may need to map. The three genes you have shown here don't map, and of those t…
Votes
C: when to apply quantile normalization with voom in limma/voom framework with RNA-
A: How to know if I should use voomWithQualityWeights() or not?
A: Weird results (ribosomal proteins / Y-linked genes) in limma/voom
Answer: Log-cpm values from limma
Answer: Log-cpm values from limma
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