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Showing :
recount3
•
reset
0
votes
3
replies
628
views
Merging multi-fastq samples in recount3
recount3
written 7 months ago by
Charlotte Capitanchik
• 0
0
votes
4
replies
1.0k
views
Recount3: PCR duplicates
pcrduplicates
recount3
multimappingreads
updated 7 months ago by
ATpoint
★ 4.7k • written 22 months ago by
seline.natalie
• 0
0
votes
1
reply
661
views
Recount3 error downloading data
recount3
recount
updated 9 months ago by
Leonardo Collado Torres
★ 1.1k • written 13 months ago by
Max Bone
• 0
4
votes
3
replies
801
views
recount3 problem downloading data from source sra
recount3
updated 10 months ago by
Leonardo Collado Torres
★ 1.1k • written 10 months ago by
PABLO ANTONIO
▴ 10
1
vote
1
reply
637
views
Transcript level expression for CCLE
recount3
recount
CCLE
updated 13 months ago by
Leonardo Collado Torres
★ 1.1k • written 13 months ago by
António Miguel de Jesus Domingues
▴ 510
0
votes
2
replies
1.0k
views
TCGA counts to TPM from recount3 do not seem to right
recount3
TCGA
RNASeq
updated 16 months ago by
Leonardo Collado Torres
★ 1.1k • written 17 months ago by
tangming2005
▴ 200
0
votes
2
replies
1.0k
views
recount3 monorail pipeline version
recount3
17 months ago • updated 15 months ago
Lorenzo
• 0
0
votes
3
replies
2.2k
views
Recount3 error with default "recount3_url" option
recount3
updated 22 months ago by
Leonardo Collado Torres
★ 1.1k • written 2.3 years ago by
Cornwell, Adam
▴ 110
0
votes
2
replies
1.2k
views
Recount3 data download problem
recount
recount3
updated 22 months ago by
Leonardo Collado Torres
★ 1.1k • written 2.3 years ago by
gamma.jian
▴ 10
2
votes
6
replies
1.8k
views
Unable to load data from duffel.rail
recount
recountWorkflow
recount3
updated 22 months ago by
Leonardo Collado Torres
★ 1.1k • written 2.3 years ago by
Max Bone
• 0
2
votes
11
replies
2.1k
views
Not able to download recount3 data
recount3
updated 22 months ago by
Leonardo Collado Torres
★ 1.1k • written 2.2 years ago by
Niveditha
▴ 20
0
votes
2
replies
1.1k
views
Cannot download data from IDIES links
recount
recountWorkflow
recount3
updated 22 months ago by
Leonardo Collado Torres
★ 1.1k • written 2.2 years ago by
dml
• 0
1
vote
3
replies
1.6k
views
Can i perform DEseq2 from 2 different rse objects download from RECOUNT database
DESeq2
recount
GTEx
TCGA
recount3
updated 22 months ago by
ATpoint
★ 4.7k • written 22 months ago by
David
▴ 20
1
vote
3
replies
1.0k
views
Recount3 data correspond to TCGA data
recount3
updated 8 weeks ago by
Leonardo Collado Torres
★ 1.1k • written 23 months ago by
kevin lee
• 0
2
votes
3
replies
1.3k
views
BigWig files provided by recount3
recount3
updated 2.0 years ago by
Leonardo Collado Torres
★ 1.1k • written 2.0 years ago by
mario.keller.1988
▴ 20
4
votes
6
replies
1.4k
views
recount 3 protect read length metadata
recountWorkflow
recount3
updated 2.2 years ago by
Leonardo Collado Torres
★ 1.1k • written 2.3 years ago by
soever
▴ 20
1
vote
1
reply
1.1k
views
searching study metadata in recount3
recount3
updated 2.4 years ago by
Leonardo Collado Torres
★ 1.1k • written 2.4 years ago by
andrew.su
▴ 10
0
votes
1
reply
1.1k
views
recount3 transform_counts vs compute_read_counts
recount3
updated 2.6 years ago by
Leonardo Collado Torres
★ 1.1k • written 2.6 years ago by
fdelillo
• 0
2
votes
2
replies
2.7k
views
Create TPM gene tables/dataframe from ReCount3
recount3
TCGA
GTEx
DESeq2
2.8 years ago
David
▴ 20
10
votes
11
replies
3.4k
views
Counts from recount3 for DESeq2 analysis
recount3
DESeq2
updated 2.6 years ago by
Leonardo Collado Torres
★ 1.1k • written 2.9 years ago by
william.benit
▴ 10
0
votes
2
replies
1.3k
views
Missing sample in recount3 data
recount3
3.0 years ago • updated 2.9 years ago
alex.dietrich
• 0
0
votes
1
reply
1.2k
views
Retrieve the read counts per transcript instead of per gene
recount3
updated 3.0 years ago by
Leonardo Collado Torres
★ 1.1k • written 3.0 years ago by
oligoelemento
▴ 10
11
votes
8
replies
2.6k
views
Error when downloading data with recount3.
recount3
updated 3.0 years ago by
chris.wilks
▴ 70 • written 4.4 years ago by
Zach Brehm
▴ 20
1
vote
1
reply
1.7k
views
recount3 - download bigwig files for TCGA data
recount3
recount
TCGA
updated 3.0 years ago by
Leonardo Collado Torres
★ 1.1k • written 3.0 years ago by
Xuebing
▴ 10
0
votes
1
reply
825
views
Sample tissue annotation
recount3
updated 3.1 years ago by
Leonardo Collado Torres
★ 1.1k • written 3.1 years ago by
M.M.M.M.
• 0
0
votes
1
reply
1.1k
views
Distinguishing between single cell and bulk data in recount3 study explorer
recount3
updated 3.1 years ago by
Leonardo Collado Torres
★ 1.1k • written 3.3 years ago by
kstachelek
• 0
0
votes
2
replies
2.3k
views
Get read counts for TCGA samples via recount3
recount3
3.4 years ago • updated 3.3 years ago
mario.keller.1988
▴ 20
2
votes
2
replies
1.7k
views
[recount3] Merge gene counts tables from multiple projects (SRP)
recount3
recountWorkflow
updated 3.4 years ago by
Leonardo Collado Torres
★ 1.1k • written 3.5 years ago by
António Miguel de Jesus Domingues
▴ 510
0
votes
1
reply
1.1k
views
Different read support for splice junctions using snapcount and recount3
recount3
snapcount
updated 3.4 years ago by
Leonardo Collado Torres
★ 1.1k • written 3.5 years ago by
mario.keller.1988
▴ 20
2
votes
5
replies
1.8k
views
Downloading count matrix for full recount3 dataset
recount3
updated 12 months ago by
Leonardo Collado Torres
★ 1.1k • written 3.7 years ago by
Ben
• 0
0
votes
2
replies
1.4k
views
recount3: advice for working with an unannotated genes
recount3
updated 3.3 years ago by
devorah.fialkoff
• 0 • written 3.8 years ago by
MakeTheBrain
• 0
1
vote
1
reply
2.1k
views
Correlation analyses on TCGA data
RNA-seq
Normalization
edgeR
recount3
updated 3.8 years ago by
Leonardo Collado Torres
★ 1.1k • written 3.8 years ago by
mario.keller.1988
▴ 20
0
votes
1
reply
1.5k
views
Using recount data to calculate Intron retention
snapcount
recount3
recount
updated 4.0 years ago by
Leonardo Collado Torres
★ 1.1k • written 4.0 years ago by
Mariela Cortés López
• 0
33 results • Page
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Comment: DiffBind custom normalization factor
by
Abbie
• 0
Hello! Thanks so much for adding dba.normalize and all the documentation in the manual! I'm hoping I can ask a follow-up question here. I…
Answer: CpGs with genomic positions greater than the chromosome size in EPICv2?
by
James W. MacDonald
68k
All of the annotation packages provided by Bioconductor are simply repackaging of existing data from one or more sources. In this case, the…
Comment: Using TPM from tximport of Salmon output for singscore
by
Kent
• 0
Thank you for the suggestions Michael. Would you say that after filtering out the low count genes, `rlog(counts, blind = T)` is doing the s…
Comment: Using TPM from tximport of Salmon output for singscore
by
Michael Love
43k
For clustering generally we recommend `vst()` see the workflow for example. For working with individual samples, I can see how a scaling/t…
Comment: DESeq2 model - How to test case/control time course model when taking account wi
by
Michael Love
43k
I'd recommend working with a local statistician or someone familiar with linear models in R. I have to reserve my time on the support site …
Votes
clusterProfiler-GO enrichment Error
A: Machine learning in R book
Data preparation and Machine learning on time course RNAseq data
Data preparation and Machine learning on time course RNAseq data
Answer: Use of org.Rn.eg.db with GRCr8 reference genome
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