Showing : recount • reset
0
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1.1k
views
recount
recount
updated 6 months ago by ★ 1.1k • written 2.8 years ago by • 0
0
votes
1
reply
640
views
Recount3 error downloading data
recount3 recount
updated 8 months ago by ★ 1.1k • written 13 months ago by • 0
1
vote
1
reply
611
views
Transcript level expression for CCLE
recount3 recount CCLE
updated 13 months ago by ★ 1.1k • written 13 months ago by ▴ 510
2
votes
1
reply
770
views
Zero counts for all samples for all genes downloaded from recount3
recount
updated 19 months ago by ★ 4.7k • written 19 months ago by ▴ 10
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2
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1.1k
views
Recount3 data download problem
recount recount3
updated 22 months ago by ★ 1.1k • written 2.2 years ago by ▴ 10
2
votes
6
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1.8k
views
Unable to load data from duffel.rail
recount recountWorkflow recount3
updated 22 months ago by ★ 1.1k • written 2.2 years ago by • 0
0
votes
2
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1.0k
views
Cannot download data from IDIES links
recount recountWorkflow recount3
updated 22 months ago by ★ 1.1k • written 2.2 years ago by • 0
1
vote
3
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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 ★ 4.7k • written 22 months ago by ▴ 20
1
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1
reply
1.6k
views
recount3 - download bigwig files for TCGA data
recount3 recount TCGA
updated 2.9 years ago by ★ 1.1k • written 2.9 years ago by ▴ 10
1
vote
4
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4.6k
views
NA values of count matrix in class DESeqDataSet
rna-seq recount
updated 3.9 years ago by ★ 1.1k • written 7.4 years ago by • 0
0
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1
reply
1.5k
views
Using recount data to calculate Intron retention
snapcount recount3 recount
updated 3.9 years ago by ★ 1.1k • written 3.9 years ago by • 0
0
votes
2
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1.8k
views
Recount2 Bigwigs for TCGA
R TCGA recount2 recount
updated 4.9 years ago by ★ 1.1k • written 5.0 years ago by • 0
0
votes
1
reply
932
views
recount: inconsistency between pheno table structure for gene and transcript datasets
software error recount
updated 5.2 years ago by ★ 1.1k • written 5.2 years ago by • 0
4
votes
7
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2.0k
views
recount TCGA data one gene_id mapped to multiple symbols and vice versa
recount
updated 5.3 years ago by ★ 1.1k • written 5.3 years ago by ▴ 20
0
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4
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1.7k
views
Inconsistent geo_char for rse_tx
bug recount
6.2 years ago • updated 5.4 years ago Jacques.van-Helden • 0
0
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1
reply
1.0k
views
How to identify all SRPs with GTEx bigwig files?
recount
5.5 years ago hyp15 • 0
0
votes
2
replies
2.1k
views
Obtaining recount project data in TPM?
recount
updated 5.5 years ago by ★ 1.1k • written 5.5 years ago by • 0
3
votes
4
replies
1.7k
views
What assays are distributed with Recount TX data
recount recount2 RangedSummarizedExperiment
updated 5.5 years ago by ★ 1.1k • written 6.3 years ago by ▴ 120
1
vote
6
replies
1.9k
views
how to download bigwig from recount2?
recount
updated 5.6 years ago by 25k • written 5.6 years ago by • 0
1
vote
5
replies
1.9k
views
scale_counts targetSize normalization for recount2 counts
recount
updated 5.7 years ago by ★ 1.1k • written 5.7 years ago by • 0
0
votes
3
replies
2.2k
views
Problem constructing DESeq objects with large integers.
deseq2 recount
5.8 years ago Zach Brehm • 0
3
votes
3
replies
1.7k
views
Recount data for unannotated genes
recount RNAseq gencode lncRNA gene annotation
updated 5.9 years ago by ▴ 70 • written 5.9 years ago by ▴ 20
1
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1
reply
1.2k
views
Number of reads from recount are greater than target library size (40 million) for TCGA and GTEx projects
recount
updated 5.9 years ago by ★ 1.1k • written 5.9 years ago by ▴ 20
0
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1
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3.8k
views
Is GTEx age and sex data available via the recount package?
recount gtex
updated 6.4 years ago by ★ 1.1k • written 6.4 years ago by • 0
0
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1
reply
1.2k
views
What does scaling RNASeq data using the area under coverage information (AUC) mean ? - related to recount package
library size factor recount
updated 6.4 years ago by ★ 1.1k • written 6.5 years ago by • 0
0
votes
3
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1.4k
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 7.0 years ago by ★ 1.1k • written 7.0 years ago by • 0
0
votes
2
replies
1.3k
views
Recount2 TCGA metadata missing sample, run and experiment columns
recount metadata tcga
updated 7.0 years ago by • 0 • written 7.0 years ago by • 0
3
votes
3
replies
2.1k
views
derfinder: how to merge regions and counts from individual chromosomes
derfinder recount
updated 7.3 years ago by ★ 1.1k • written 7.3 years ago by ▴ 510
0
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1
reply
1.4k
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 7.3 years ago by ★ 1.1k • written 7.3 years ago by • 0
0
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1
reply
3.4k
views
NA values of count matrix in class DESeqDataSet
rnaseq recount
7.4 years ago maleknias • 0
0
votes
1
reply
2.4k
views
Recount TCGA data
recount
updated 7.5 years ago by ★ 1.1k • written 7.5 years ago by • 0
0
votes
5
replies
2.6k
views
Matching columns to sample names
recount
updated 7.5 years ago by ★ 1.1k • written 7.5 years ago by • 0
2
votes
2
replies
1.7k
views
Number of IRanges elements in TCGA HiSeqV2 dataset
r tcga recount iranges
updated 7.7 years ago by ★ 1.1k • written 7.7 years ago by ▴ 20
3
votes
10
replies
2.3k
views
recount counts in the example experiment
recount
updated 7.8 years ago by ★ 1.1k • written 7.8 years ago by 43k
2
votes
1
reply
1.5k
views
recount not available
recount
updated 7.9 years ago by 25k • written 7.9 years ago by ★ 1.0k
2
votes
4
replies
2.5k
views
TCGA - Different Sample Number
recount
updated 8.0 years ago by ▴ 20 • written 8.0 years ago by • 0
0
votes
14
replies
3.9k
views
Error through importing (project = 'SRP009615') or even to download any BigWig File
recount Tutorial
updated 8.0 years ago by ★ 1.1k • written 8.0 years ago by • 0
1
vote
4
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3.3k
views
The recount package is not available for R version 3.3.1
recount
8.5 years ago arjunkrish • 0
38 results • Page 1 of 1
Recent ...
Replies
Comment: how many significant figures are there in DESeq2 output by ATpoint ★ 4.7k
If you want consistency then use a fixed software environment like Docker, wirh fixed code and thresholds that make sense. Rounding to near…
Comment: Compare TCGA-PAAD with GTEx gene expression by Jane • 0
why aren't there any answers?
Comment: Too many significant genes when integrating gtex and tcga by Jane • 0
I encountered the same issue: too many DEGs after limma analysis. It is sad that until today we can still see the paper published where GTE…
Comment: how many significant figures are there in DESeq2 output by Matthew McCormack ▴ 180
Thank you for your reply. It is good to know that cutoff of 0.05 means less than 0.05. My concerns are about consistency and reproducibili…
Comment: DiffBind edgeR normalization --- why are the normalization factors all equal to by ATpoint ★ 4.7k
No, normalization factors from edgeR rather than size factors from DESeq2 are not proportional, it's a different concept and implementation…
Votes
A: Unbalanced experiment with multiple samples from each patient.
Unbalanced experiment with multiple samples from each patient.
Answer: Vertical line at A=0, nothing else, on MA plot
Answer: GSVA Error Code "Calling gsva(expr=., gset.idx.list=., method=., ...) is defunct
Answer: Group-specific condition effects with individuals nested: matrix is not full ra
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