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Showing :
recount3
•
reset
0
votes
3
replies
507
views
Merging multi-fastq samples in recount3
recount3
written 3 months ago by
Charlotte Capitanchik
• 0
0
votes
4
replies
943
views
Recount3: PCR duplicates
pcrduplicates
recount3
multimappingreads
updated 3 months ago by
ATpoint
★ 4.5k • written 17 months ago by
seline.natalie
• 0
0
votes
1
reply
510
views
Recount3 error downloading data
recount3
recount
updated 5 months ago by
Leonardo Collado Torres
★ 1.1k • written 9 months ago by
Max Bone
• 0
4
votes
3
replies
618
views
recount3 problem downloading data from source sra
recount3
updated 5 months ago by
Leonardo Collado Torres
★ 1.1k • written 5 months ago by
PABLO ANTONIO
▴ 10
1
vote
1
reply
488
views
Transcript level expression for CCLE
recount3
recount
CCLE
updated 9 months ago by
Leonardo Collado Torres
★ 1.1k • written 9 months ago by
António Miguel de Jesus Domingues
▴ 510
0
votes
2
replies
838
views
TCGA counts to TPM from recount3 do not seem to right
recount3
TCGA
RNASeq
updated 12 months ago by
Leonardo Collado Torres
★ 1.1k • written 12 months ago by
tangming2005
▴ 200
0
votes
2
replies
884
views
recount3 monorail pipeline version
recount3
13 months ago • updated 11 months ago
Lorenzo
• 0
0
votes
3
replies
1.9k
views
Recount3 error with default "recount3_url" option
recount3
updated 18 months ago by
Leonardo Collado Torres
★ 1.1k • written 23 months ago by
Cornwell, Adam
▴ 110
0
votes
2
replies
1.1k
views
Recount3 data download problem
recount
recount3
updated 18 months ago by
Leonardo Collado Torres
★ 1.1k • written 23 months ago by
gamma.jian
▴ 10
2
votes
6
replies
1.6k
views
Unable to load data from duffel.rail
recount
recountWorkflow
recount3
updated 18 months ago by
Leonardo Collado Torres
★ 1.1k • written 23 months ago by
Max Bone
• 0
2
votes
11
replies
2.0k
views
Not able to download recount3 data
recount3
updated 18 months ago by
Leonardo Collado Torres
★ 1.1k • written 23 months ago by
Niveditha
▴ 20
0
votes
2
replies
963
views
Cannot download data from IDIES links
recount
recountWorkflow
recount3
updated 18 months ago by
Leonardo Collado Torres
★ 1.1k • written 23 months ago by
dml
• 0
1
vote
3
replies
1.4k
views
Can i perform DEseq2 from 2 different rse objects download from RECOUNT database
DESeq2
recount
GTEx
TCGA
recount3
updated 18 months ago by
ATpoint
★ 4.5k • written 18 months ago by
David
▴ 20
0
votes
1
reply
761
views
Recount3 data correspond to TCGA data
recount3
updated 17 months ago by
seline.natalie
• 0 • written 19 months ago by
kevin lee
• 0
2
votes
3
replies
1.1k
views
BigWig files provided by recount3
recount3
updated 20 months ago by
Leonardo Collado Torres
★ 1.1k • written 20 months ago by
mario.keller.1988
▴ 20
4
votes
6
replies
1.3k
views
recount 3 protect read length metadata
recountWorkflow
recount3
updated 21 months ago by
Leonardo Collado Torres
★ 1.1k • written 23 months ago by
soever
▴ 20
1
vote
1
reply
957
views
searching study metadata in recount3
recount3
updated 2.0 years ago by
Leonardo Collado Torres
★ 1.1k • written 2.1 years ago by
andrew.su
▴ 10
0
votes
1
reply
950
views
recount3 transform_counts vs compute_read_counts
recount3
updated 2.2 years ago by
Leonardo Collado Torres
★ 1.1k • written 2.2 years ago by
fdelillo
• 0
2
votes
2
replies
2.4k
views
Create TPM gene tables/dataframe from ReCount3
recount3
TCGA
GTEx
DESeq2
2.4 years ago
David
▴ 20
10
votes
11
replies
3.0k
views
Counts from recount3 for DESeq2 analysis
recount3
DESeq2
updated 2.2 years ago by
Leonardo Collado Torres
★ 1.1k • written 2.6 years ago by
william.benit
▴ 10
0
votes
2
replies
1.2k
views
Missing sample in recount3 data
recount3
2.7 years ago • updated 2.6 years ago
alex.dietrich
• 0
0
votes
1
reply
1.1k
views
Retrieve the read counts per transcript instead of per gene
recount3
updated 2.6 years ago by
Leonardo Collado Torres
★ 1.1k • written 2.7 years ago by
oligoelemento
▴ 10
11
votes
8
replies
2.5k
views
Error when downloading data with recount3.
recount3
updated 2.6 years ago by
chris.wilks
▴ 70 • written 4.0 years ago by
Zach Brehm
▴ 20
1
vote
1
reply
1.4k
views
recount3 - download bigwig files for TCGA data
recount3
recount
TCGA
updated 2.6 years ago by
Leonardo Collado Torres
★ 1.1k • written 2.6 years ago by
Xuebing
▴ 10
0
votes
1
reply
771
views
Sample tissue annotation
recount3
updated 2.7 years ago by
Leonardo Collado Torres
★ 1.1k • written 2.8 years ago by
M.M.M.M.
• 0
0
votes
1
reply
1.0k
views
Distinguishing between single cell and bulk data in recount3 study explorer
recount3
updated 2.7 years ago by
Leonardo Collado Torres
★ 1.1k • written 2.9 years ago by
kstachelek
• 0
0
votes
2
replies
2.0k
views
Get read counts for TCGA samples via recount3
recount3
3.0 years ago
mario.keller.1988
▴ 20
2
votes
2
replies
1.5k
views
[recount3] Merge gene counts tables from multiple projects (SRP)
recount3
recountWorkflow
updated 3.1 years ago by
Leonardo Collado Torres
★ 1.1k • written 3.1 years ago by
António Miguel de Jesus Domingues
▴ 510
0
votes
1
reply
994
views
Different read support for splice junctions using snapcount and recount3
recount3
snapcount
updated 3.1 years ago by
Leonardo Collado Torres
★ 1.1k • written 3.1 years ago by
mario.keller.1988
▴ 20
2
votes
5
replies
1.6k
views
Downloading count matrix for full recount3 dataset
recount3
updated 8 months ago by
Leonardo Collado Torres
★ 1.1k • written 3.4 years ago by
Ben
• 0
0
votes
2
replies
1.3k
views
recount3: advice for working with an unannotated genes
recount3
updated 3.0 years ago by
devorah.fialkoff
• 0 • written 3.5 years ago by
MakeTheBrain
• 0
1
vote
1
reply
1.9k
views
Correlation analyses on TCGA data
RNA-seq
Normalization
edgeR
recount3
updated 3.5 years ago by
Leonardo Collado Torres
★ 1.1k • written 3.5 years ago by
mario.keller.1988
▴ 20
0
votes
1
reply
1.4k
views
Using recount data to calculate Intron retention
snapcount
recount3
recount
updated 3.6 years ago by
Leonardo Collado Torres
★ 1.1k • written 3.6 years ago by
Mariela Cortés López
• 0
33 results • Page
1 of 1
Recent ...
Replies
Comment: Appropriate ways to filter counts data for voom/limma
by
dorothylminter
• 0
The proper way to filter count data for voom/limma emphasizes the importance of choosing the right filtering technique to enhance detection…
Comment: How to extract phastcons score for all protein coding genes and lncRNAs using Ge
by
Robert Castelo
★ 3.4k
Hi, this is a long comment thread on 4-year old post, please open a new post with you question. To increase the odds of getting useful answ…
Comment: DESeq2 rerun returns different results
by
ATpoint
★ 4.5k
DESeq2 is deterministic if you use same input, code and software versions. Make sure to version-control your environment by at least tracki…
Answer: [How to construct a model.matrix ]
by
Gordon Smyth
51k
> Initially, I simply used > `lm(Epigenetic_age ~ Age_group + Age + Sex + PC1 + PC2 + PC3 + PC4 + PC5 + B + CD4T + CD8T + Mono + NK + Neutr…
Comment: How to extract phastcons score for all protein coding genes and lncRNAs using Ge
by
rania.alanany
• 0
Hi Robert, Thank you for the explanation, But I am still little bit confused, Is the annotation package (TxDb.Hsapiens.UCSC.hg38.knownGene)…
Votes
A: Some questions for remove batch effect by using mnnCorrect
A: Recommendations for combining multiple 10x runs into one SingleCellExperiment
Answer: [How to construct a model.matrix ]
Answer: Handling biological replicates in DESeq2
Comment: biomaRt rnorvegicus_gene_ensembl not available anymore
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Robert Castelo
★ 3.4k
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to
Michael Stadler
▴ 350
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to
ATpoint
★ 4.5k
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to
James W. MacDonald
67k
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to
Stefano Mangiola
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