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Showing :
recount
•
reset
0
votes
0
replies
174
views
Recount3 error downloading data
recount3
recount
12 weeks ago
Max Bone
• 0
1
vote
1
reply
214
views
Transcript level expression for CCLE
recount3
recount
CCLE
updated 3 months ago by
Leonardo Collado Torres
★ 1.0k • written 3 months ago by
António Miguel de Jesus Domingues
▴ 510
2
votes
1
reply
473
views
Zero counts for all samples for all genes downloaded from recount3
recount
updated 8 months ago by
ATpoint
★ 4.1k • written 8 months ago by
urwah
▴ 10
0
votes
2
replies
798
views
Recount3 data download problem
recount
recount3
updated 12 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 12 months ago by
Leonardo Collado Torres
★ 1.0k • written 17 months ago by
Max Bone
• 0
0
votes
2
replies
689
views
Cannot download data from IDIES links
recount
recountWorkflow
recount3
updated 12 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 12 months ago by
ATpoint
★ 4.1k • written 12 months ago by
David
▴ 20
0
votes
1
reply
718
views
recount
recount
updated 24 months ago by
Henry
• 0 • written 24 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 4.2 years ago by
alex.v.nesta
• 0
0
votes
1
reply
742
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
792
views
How to identify all SRPs with GTEx bigwig files?
recount
4.7 years ago
hyp15
• 0
0
votes
2
replies
1.7k
views
Obtaining recount project data in TPM?
recount
updated 4.7 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 4.7 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
1.9k
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
955
views
Number of reads from recount are greater than target library size (40 million) for TCGA and GTEx projects
recount
updated 5.1 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
▴ 510
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 7.2 years ago by
sellis18
▴ 20 • written 7.2 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: Differences in differential analysis methods for RNA-Seq
by
ATpoint
★ 4.1k
> I am just re-processing due to being uncertain about how they used the edgeR analysis to reach gene level edgeR devs published something…
Comment: Differences in differential analysis methods for RNA-Seq
by
james.zhang20
• 0
Thanks for the explanations, it has helped clarify some things. Unfortunately, I am working from an early access public dataset (https://do…
Comment: Deseq2 and Normalization of RNA sequencing data
by
ATpoint
★ 4.1k
There is no expectation of normality that is realistic in terms of expression level. Levels are widely different between genes, and counts …
Comment: Differences in differential analysis methods for RNA-Seq
by
ATpoint
★ 4.1k
MAGeCK is a command line tool that is easy to use. I recommend you use it because a) the logFCs from DESeq2 and MAGeCK will be very similar…
Comment: Get genomic coordinates of CpGs sites (chromosomes, genomic position)
by
Yveto
• 0
Thank for your response. It is Illumina 450 K. I use this code ```{r } library(IlluminaHumanMethylation450kanno.ilmn12.hg19) annotat…
Votes
A: Error in DESeqDataSet : some values in assay are not integers
Bioconductor 3.19 is Released!
Bioconductor 3.19 is Released!
Answer: DEseq2 coefficient
SPIA plotP giving error
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