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Showing :
recount
•
reset
0
votes
0
replies
168
views
Recount3 error downloading data
recount3
recount
11 weeks ago
Max Bone
• 0
1
vote
1
reply
202
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
2
votes
1
reply
466
views
Zero counts for all samples for all genes downloaded from recount3
recount
updated 8 months ago by
ATpoint
★ 4.0k • written 8 months ago by
urwah
▴ 10
0
votes
2
replies
790
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
0
votes
2
replies
679
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
1.0k
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
715
views
recount
recount
updated 23 months ago by
Henry
• 0 • written 23 months ago by
nathan-temple
• 0
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
1
vote
4
replies
3.8k
views
NA values of count matrix in class DESeqDataSet
rna-seq
recount
updated 3.0 years ago by
Leonardo Collado Torres
★ 1.0k • written 6.6 years ago by
maleknias
• 0
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
0
votes
2
replies
1.4k
views
Recount2 Bigwigs for TCGA
R
TCGA
recount2
recount
updated 4.1 years ago by
Leonardo Collado Torres
★ 1.0k • written 4.1 years ago by
alex.v.nesta
• 0
0
votes
1
reply
738
views
recount: inconsistency between pheno table structure for gene and transcript datasets
software error
recount
updated 4.4 years ago by
Leonardo Collado Torres
★ 1.0k • written 4.4 years ago by
Jacques.van-Helden
• 0
4
votes
7
replies
1.6k
views
recount TCGA data one gene_id mapped to multiple symbols and vice versa
recount
updated 4.5 years ago by
Leonardo Collado Torres
★ 1.0k • written 4.5 years ago by
Sheldon Pang
▴ 20
0
votes
4
replies
1.3k
views
Inconsistent geo_char for rse_tx
bug
recount
5.3 years ago • updated 4.5 years ago
Jacques.van-Helden
• 0
0
votes
1
reply
788
views
How to identify all SRPs with GTEx bigwig files?
recount
4.6 years ago
hyp15
• 0
0
votes
2
replies
1.6k
views
Obtaining recount project data in TPM?
recount
updated 4.6 years ago by
Leonardo Collado Torres
★ 1.0k • written 4.7 years ago by
codden.c
• 0
3
votes
4
replies
1.4k
views
What assays are distributed with Recount TX data
recount
recount2
RangedSummarizedExperiment
updated 4.6 years ago by
Leonardo Collado Torres
★ 1.0k • written 5.5 years ago by
k.vitting.seerup
▴ 120
1
vote
6
replies
1.6k
views
how to download bigwig from recount2?
recount
updated 4.7 years ago by
Martin Morgan
25k • written 4.7 years ago by
hyp15
• 0
1
vote
5
replies
1.5k
views
scale_counts targetSize normalization for recount2 counts
recount
updated 4.9 years ago by
Leonardo Collado Torres
★ 1.0k • written 4.9 years ago by
sidreed34
• 0
0
votes
3
replies
1.8k
views
Problem constructing DESeq objects with large integers.
deseq2
recount
5.0 years ago
Zach Brehm
• 0
3
votes
3
replies
1.3k
views
Recount data for unannotated genes
recount
RNAseq
gencode
lncRNA
gene annotation
updated 5.0 years ago by
chris.wilks
▴ 70 • written 5.1 years ago by
francesco.gandolfi
▴ 20
1
vote
1
reply
950
views
Number of reads from recount are greater than target library size (40 million) for TCGA and GTEx projects
recount
updated 5.0 years ago by
Leonardo Collado Torres
★ 1.0k • written 5.1 years ago by
Sheldon Pang
▴ 20
0
votes
1
reply
3.3k
views
Is GTEx age and sex data available via the recount package?
recount
gtex
updated 5.5 years ago by
Leonardo Collado Torres
★ 1.0k • written 5.5 years ago by
abe
• 0
0
votes
1
reply
1.0k
views
What does scaling RNASeq data using the area under coverage information (AUC) mean ? - related to recount package
library size factor
recount
updated 5.6 years ago by
Leonardo Collado Torres
★ 1.0k • written 5.7 years ago by
elmahy2005
• 0
0
votes
3
replies
1.2k
views
According to Recount2 metadata and Recount2 website, SRP000941 has 345 samples, but after downloading the study the rse_gene object only has 343 samp…
recount
updated 6.1 years ago by
Leonardo Collado Torres
★ 1.0k • written 6.1 years ago by
Kayla
• 0
0
votes
2
replies
1.1k
views
Recount2 TCGA metadata missing sample, run and experiment columns
recount
metadata
tcga
updated 6.2 years ago by
rosabellascottgm
• 0 • written 6.2 years ago by
Mariela Cortés-López
• 0
3
votes
3
replies
1.7k
views
derfinder: how to merge regions and counts from individual chromosomes
derfinder
recount
updated 6.4 years ago by
Leonardo Collado Torres
★ 1.0k • written 6.4 years ago by
António Miguel de Jesus Domingues
▴ 490
0
votes
1
reply
1.2k
views
Getting pheno tables from recount datasets without any NA values in characteristics and geo_accession fields and also without duplicated row.names
recount
summarizedexperiment
updated 6.5 years ago by
Leonardo Collado Torres
★ 1.0k • written 6.5 years ago by
Mustafa ABUELQUMSAN
• 0
0
votes
1
reply
3.0k
views
NA values of count matrix in class DESeqDataSet
rnaseq
recount
6.6 years ago
maleknias
• 0
0
votes
1
reply
1.9k
views
Recount TCGA data
recount
updated 6.6 years ago by
Leonardo Collado Torres
★ 1.0k • written 6.6 years ago by
rajesha1986
• 0
0
votes
5
replies
1.9k
views
Matching columns to sample names
recount
updated 6.7 years ago by
Leonardo Collado Torres
★ 1.0k • written 6.7 years ago by
b.curran
• 0
2
votes
2
replies
1.4k
views
Number of IRanges elements in TCGA HiSeqV2 dataset
r
tcga
recount
iranges
updated 6.9 years ago by
Leonardo Collado Torres
★ 1.0k • written 6.9 years ago by
biomiha
▴ 20
3
votes
10
replies
2.0k
views
recount counts in the example experiment
recount
updated 7.0 years ago by
Leonardo Collado Torres
★ 1.0k • written 7.0 years ago by
Michael Love
41k
2
votes
1
reply
1.3k
views
recount not available
recount
updated 7.0 years ago by
Martin Morgan
25k • written 7.0 years ago by
Stephen Henderson
★ 1.0k
2
votes
4
replies
2.1k
views
TCGA - Different Sample Number
recount
updated 7.1 years ago by
sellis18
▴ 20 • written 7.1 years ago by
iedenkim
• 0
0
votes
14
replies
3.2k
views
Error through importing (project = 'SRP009615') or even to download any BigWig File
recount
Tutorial
updated 7.2 years ago by
Leonardo Collado Torres
★ 1.0k • written 7.2 years ago by
Mustafa ABUELQUMSAN
• 0
1
vote
4
replies
3.0k
views
The recount package is not available for R version 3.3.1
recount
7.7 years ago
arjunkrish
• 0
38 results • Page
1 of 1
Recent ...
Replies
Comment: Math expression in shapeCustom legend in EnhancedVolcano
by
pl23
• 0
Thank you very much - that worked perfectly! Word of warning to those who try this: it screws up the other legends because of the markdown …
Answer: PCA plot suggestions
by
Michael Love
41k
For help with interpretation and design of analysis, I recommend working with a local statistician. Due to time restrictions, I can only…
Comment: DESeq2 Error in `.rowNamesDF<-`(x, value = value): Invalid 'row.names' length
by
ussarizona
▴ 10
Hi Michael, Yes, I could figure it out what does the error mean. In my matrix I had the first colum GeneID while in my condition I only h…
Answer: Deseq2. decontXcounts not integers. Useful alternative?
by
Michael Love
41k
Another option would be to put the per sample estimated contamination in the design. This is for example how RUV etc help remove spurious D…
Answer: ATACseq merge peaks
by
ATpoint
★ 4.0k
That depends on your analysis. Typically, for differential analysis (and convenience) you would produce a single set of peaks (e.g. by merg…
Votes
Answer: Math expression in shapeCustom legend in EnhancedVolcano
Comment: DESeq2 Error in `.rowNamesDF<-`(x, value = value): Invalid 'row.names' length
Comment: Deseq2. decontXcounts not integers. Useful alternative?
Comment: Opposite sign of LFC in count plots of DEGs (DESeq2)
biomaRt error: database disk image is malformed
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