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recount3
•
reset
0
votes
0
replies
35
views
Junction CPM via Snapcount and Recount3
snapcount
recount3
3 days ago
henry.tietz
• 0
0
votes
1
reply
1.4k
views
Retrieve Salmon transcript quantification file from recount3
recount3
updated 7 months ago by
Leonardo Collado Torres
★ 1.1k • written 7 months ago by
kyn
▴ 10
0
votes
3
replies
998
views
Merging multi-fastq samples in recount3
recount3
written 17 months ago by
Charlotte Capitanchik
• 0
0
votes
4
replies
1.4k
views
Recount3: PCR duplicates
pcrduplicates
recount3
multimappingreads
updated 17 months ago by
ATpoint
★ 5.0k • written 2.6 years ago by
seline.natalie
• 0
0
votes
1
reply
930
views
Recount3 error downloading data
recount3
recount
updated 19 months ago by
Leonardo Collado Torres
★ 1.1k • written 23 months ago by
Max Bone
• 0
4
votes
3
replies
1.2k
views
recount3 problem downloading data from source sra
recount3
updated 20 months ago by
Leonardo Collado Torres
★ 1.1k • written 20 months ago by
PABLO ANTONIO
▴ 10
1
vote
1
reply
1000
views
Transcript level expression for CCLE
recount3
recount
CCLE
updated 23 months ago by
Leonardo Collado Torres
★ 1.1k • written 23 months ago by
António Miguel de Jesus Domingues
▴ 510
0
votes
2
replies
1.4k
views
TCGA counts to TPM from recount3 do not seem to right
recount3
TCGA
RNASeq
updated 2.2 years ago by
Leonardo Collado Torres
★ 1.1k • written 2.2 years ago by
tangming2005
▴ 200
0
votes
2
replies
1.3k
views
recount3 monorail pipeline version
recount3
2.3 years ago • updated 2.1 years ago
Lorenzo
• 0
0
votes
3
replies
2.5k
views
Recount3 error with default "recount3_url" option
recount3
updated 2.7 years ago by
Leonardo Collado Torres
★ 1.1k • written 3.1 years ago by
Cornwell, Adam
▴ 110
0
votes
2
replies
1.4k
views
Recount3 data download problem
recount
recount3
updated 2.7 years ago by
Leonardo Collado Torres
★ 1.1k • written 3.1 years ago by
gamma.jian
▴ 10
2
votes
6
replies
2.3k
views
Unable to load data from duffel.rail
recount
recountWorkflow
recount3
updated 2.7 years ago by
Leonardo Collado Torres
★ 1.1k • written 3.1 years ago by
Max Bone
• 0
2
votes
11
replies
2.8k
views
Not able to download recount3 data
recount3
updated 2.7 years ago by
Leonardo Collado Torres
★ 1.1k • written 3.1 years ago by
Niveditha
▴ 20
0
votes
2
replies
1.3k
views
Cannot download data from IDIES links
recount
recountWorkflow
recount3
updated 2.7 years ago by
Leonardo Collado Torres
★ 1.1k • written 3.1 years ago by
dml
• 0
1
vote
3
replies
2.0k
views
Can i perform DEseq2 from 2 different rse objects download from RECOUNT database
DESeq2
recount
GTEx
TCGA
recount3
updated 2.7 years ago by
ATpoint
★ 5.0k • written 2.7 years ago by
David
▴ 20
1
vote
3
replies
1.3k
views
Recount3 data correspond to TCGA data
recount3
updated 11 months ago by
Leonardo Collado Torres
★ 1.1k • written 2.8 years ago by
kevin lee
• 0
2
votes
3
replies
1.7k
views
BigWig files provided by recount3
recount3
updated 2.9 years ago by
Leonardo Collado Torres
★ 1.1k • written 2.9 years ago by
mario.keller.1988
▴ 20
4
votes
6
replies
1.9k
views
recount 3 protect read length metadata
recountWorkflow
recount3
updated 3.0 years ago by
Leonardo Collado Torres
★ 1.1k • written 3.1 years ago by
soever
▴ 20
1
vote
1
reply
1.4k
views
searching study metadata in recount3
recount3
updated 3.2 years ago by
Leonardo Collado Torres
★ 1.1k • written 3.2 years ago by
andrew.su
▴ 10
0
votes
1
reply
1.3k
views
recount3 transform_counts vs compute_read_counts
recount3
updated 3.4 years ago by
Leonardo Collado Torres
★ 1.1k • written 3.4 years ago by
fdelillo
• 0
2
votes
2
replies
3.7k
views
Create TPM gene tables/dataframe from ReCount3
recount3
TCGA
GTEx
DESeq2
3.6 years ago
David
▴ 20
10
votes
11
replies
4.2k
views
Counts from recount3 for DESeq2 analysis
recount3
DESeq2
updated 3.4 years ago by
Leonardo Collado Torres
★ 1.1k • written 3.7 years ago by
william.benit
▴ 10
0
votes
2
replies
1.6k
views
Missing sample in recount3 data
recount3
3.8 years ago • updated 3.7 years ago
alex.dietrich
• 0
0
votes
1
reply
1.5k
views
Retrieve the read counts per transcript instead of per gene
recount3
updated 3.8 years ago by
Leonardo Collado Torres
★ 1.1k • written 3.8 years ago by
oligoelemento
▴ 10
11
votes
8
replies
3.2k
views
Error when downloading data with recount3.
recount3
updated 3.8 years ago by
chris.wilks
▴ 70 • written 5.2 years ago by
Zach Brehm
▴ 20
1
vote
1
reply
2.2k
views
recount3 - download bigwig files for TCGA data
recount3
recount
TCGA
updated 3.8 years ago by
Leonardo Collado Torres
★ 1.1k • written 3.8 years ago by
Xuebing
▴ 10
0
votes
1
reply
1.0k
views
Sample tissue annotation
recount3
updated 3.9 years ago by
Leonardo Collado Torres
★ 1.1k • written 4.0 years ago by
M.M.M.M.
• 0
0
votes
1
reply
1.4k
views
Distinguishing between single cell and bulk data in recount3 study explorer
recount3
updated 3.9 years ago by
Leonardo Collado Torres
★ 1.1k • written 4.1 years ago by
kstachelek
• 0
0
votes
2
replies
2.9k
views
Get read counts for TCGA samples via recount3
recount3
4.2 years ago • updated 4.1 years ago
mario.keller.1988
▴ 20
2
votes
2
replies
2.1k
views
[recount3] Merge gene counts tables from multiple projects (SRP)
recount3
recountWorkflow
updated 4.2 years ago by
Leonardo Collado Torres
★ 1.1k • written 4.3 years ago by
António Miguel de Jesus Domingues
▴ 510
0
votes
1
reply
1.4k
views
Different read support for splice junctions using snapcount and recount3
recount3
snapcount
updated 4.2 years ago by
Leonardo Collado Torres
★ 1.1k • written 4.3 years ago by
mario.keller.1988
▴ 20
2
votes
5
replies
2.5k
views
Downloading count matrix for full recount3 dataset
recount3
updated 22 months ago by
Leonardo Collado Torres
★ 1.1k • written 4.5 years ago by
Ben
• 0
0
votes
2
replies
1.7k
views
recount3: advice for working with an unannotated genes
recount3
updated 4.2 years ago by
devorah.fialkoff
• 0 • written 4.6 years ago by
MakeTheBrain
• 0
1
vote
1
reply
2.4k
views
Correlation analyses on TCGA data
RNA-seq
Normalization
edgeR
recount3
updated 4.6 years ago by
Leonardo Collado Torres
★ 1.1k • written 4.6 years ago by
mario.keller.1988
▴ 20
0
votes
1
reply
1.8k
views
Using recount data to calculate Intron retention
snapcount
recount3
recount
updated 4.8 years ago by
Leonardo Collado Torres
★ 1.1k • written 4.8 years ago by
Mariela Cortés López
• 0
35 results • Page
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Answer: When to use edgeR or limma
by
James W. MacDonald
68k
I would use edgeR's quasi-likelihood model for any analysis with a smaller number of observations (like 3 vs 3 or similar), but if you have…
Answer: limpa-blank normalization and Spectronaut's PTM stoichiometry
by
Gordon Smyth
53k
limpa reads standard feature-level output from Spectronaut. You do not need to make any changes to the output before reading it into limpa.…
Comment: Question about the filterByExpr function inputs in edgeR
by
mohammedtoufiq91
▴ 10
@gordonsmyth Noted, thank you very much.
Comment: Question about the filterByExpr function inputs in edgeR
by
Gordon Smyth
53k
Regarding edgeR v4 filtering, I didn't mention anything about a minimum count of 10 but rather said "a positive count". So a minimalistic f…
Comment: limpa-blank normalization and Spectronaut's PTM stoichiometry
by
JKim
• 0
Hi Emily, He left some comments regarding normalization. Here is the relevant quote: > The EList object produced by dpcQuant(), containi…
Votes
A: deseq2 - paired samples in 2 sequencing types with very different library sizes
Comment: Question about the filterByExpr function inputs in edgeR
Answer: Question about the filterByExpr function inputs in edgeR
Answer: Question about the filterByExpr function inputs in edgeR
A: DESeq2: What is the unit of DESeq2 normalized read count (VST)? Is it tag per mi
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