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Showing :
recount3
•
reset
0
votes
0
replies
162
views
Recount3 error downloading data
recount3
recount
10 weeks ago
Max Bone
• 0
1
vote
1
reply
192
views
Transcript level expression for CCLE
recount3
recount
CCLE
updated 11 weeks ago by
Leonardo Collado Torres
★ 1.0k • written 11 weeks ago by
António Miguel de Jesus Domingues
▴ 490
0
votes
2
replies
509
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 5 months ago by
tangming2005
▴ 190
0
votes
2
replies
496
views
recount3 monorail pipeline version
recount3
6 months ago • updated 4 months ago
Lorenzo
• 0
0
votes
2
replies
486
views
Recount3: PCR duplicates
pcrduplicates
recount3
multimappingreads
updated 10 months ago by
ivanrebecca230
• 0 • written 10 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 16 months ago by
Cornwell, Adam
▴ 110
0
votes
2
replies
780
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
1.2k
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
667
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
980
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
553
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
743
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
912
views
recount 3 protect read length metadata
recountWorkflow
recount3
updated 14 months ago by
Leonardo Collado Torres
★ 1.0k • written 16 months ago by
soever
▴ 20
1
vote
1
reply
721
views
searching study metadata in recount3
recount3
updated 17 months ago by
Leonardo Collado Torres
★ 1.0k • written 18 months ago by
andrew.su
▴ 10
0
votes
1
reply
692
views
recount3 transform_counts vs compute_read_counts
recount3
updated 19 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 19 months ago by
Leonardo Collado Torres
★ 1.0k • written 2.0 years ago by
william.benit
▴ 10
0
votes
2
replies
879
views
Missing sample in recount3 data
recount3
2.1 years ago • updated 24 months ago
alex.dietrich
• 0
0
votes
1
reply
844
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
1.0k
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
637
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
833
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
2.4 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 2.5 years ago by
António Miguel de Jesus Domingues
▴ 490
0
votes
1
reply
777
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 4 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
1.1k
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
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Comment: Bioinformatics Laboratory Head in AI or machine learning (WEHI, Australia)
by
christianhilton64
• 0
I'm less familiar with the specifics of GSVA, but I'm curious about the overall goal of this analysis. Could you provide a high-level summa…
Comment: The difference when using Limma compare between 3 conditions vs 2 conditions
by
Robert Castelo
★ 3.2k
Hi, your `c2` object storing all the gene sets is probably a `list` object, where element names are the names of the pathways given by MSig…
Comment: Differential peaks that were not identified in diffbind were identified in diseq
by
lonn
• 0
I tried the default normalization and got similar results as above. Perhaps I need to try identifying the difference peak without using dif…
Answer: Cannabis and KEGGgraph
by
deeenes
▴ 30
Hello, I'm a developer of the `OmnipathR` package, and I wrote [a function][1] to access certain KEGG data: library(OmnipathR) cs…
Answer: RNAseq:Technical replicates from different batches
by
Gordon Smyth
50k
I am not entirely clear what you mean by "technical" replicates in this case. Are they resequencing of the same RNA samples or are they fre…
Votes
Installing/switching between versions of R/Rstudio/Bioconductor on personal machine (Linux | Ubuntu)
A: Docker container with bioconductor and devtools
Answer: OrgDb for maize
Comment: significant difference of p-values with dream() after updating VariancePartition
How to tell and visualize up/down regulation of pathways from clusterprofiler gsea output
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