Showing : recount • reset
0
votes
2
replies
1.2k
views
recount
recount
updated 8 months ago by ★ 1.1k • written 3.0 years ago by • 0
0
votes
1
reply
706
views
Recount3 error downloading data
recount3 recount
updated 10 months ago by ★ 1.1k • written 14 months ago by • 0
1
vote
1
reply
664
views
Transcript level expression for CCLE
recount3 recount CCLE
updated 15 months ago by ★ 1.1k • written 15 months ago by ▴ 510
2
votes
1
reply
817
views
Zero counts for all samples for all genes downloaded from recount3
recount
updated 20 months ago by ★ 4.8k • written 20 months ago by ▴ 10
0
votes
2
replies
1.2k
views
Recount3 data download problem
recount recount3
updated 23 months ago by ★ 1.1k • written 2.4 years ago by ▴ 10
2
votes
6
replies
1.9k
views
Unable to load data from duffel.rail
recount recountWorkflow recount3
updated 23 months ago by ★ 1.1k • written 2.4 years ago by • 0
0
votes
2
replies
1.1k
views
Cannot download data from IDIES links
recount recountWorkflow recount3
updated 23 months ago by ★ 1.1k • written 2.3 years ago by • 0
1
vote
3
replies
1.7k
views
Can i perform DEseq2 from 2 different rse objects download from RECOUNT database
DESeq2 recount GTEx TCGA recount3
updated 24 months ago by ★ 4.8k • written 24 months ago by ▴ 20
1
vote
1
reply
1.8k
views
recount3 - download bigwig files for TCGA data
recount3 recount TCGA
updated 3.1 years ago by ★ 1.1k • written 3.1 years ago by ▴ 10
1
vote
4
replies
4.7k
views
NA values of count matrix in class DESeqDataSet
rna-seq recount
updated 4.0 years ago by ★ 1.1k • written 7.6 years ago by • 0
0
votes
1
reply
1.5k
views
Using recount data to calculate Intron retention
snapcount recount3 recount
updated 4.1 years ago by ★ 1.1k • written 4.1 years ago by • 0
0
votes
2
replies
1.9k
views
Recount2 Bigwigs for TCGA
R TCGA recount2 recount
updated 5.1 years ago by ★ 1.1k • written 5.1 years ago by • 0
0
votes
1
reply
966
views
recount: inconsistency between pheno table structure for gene and transcript datasets
software error recount
updated 5.4 years ago by ★ 1.1k • written 5.4 years ago by • 0
4
votes
7
replies
2.1k
views
recount TCGA data one gene_id mapped to multiple symbols and vice versa
recount
updated 5.5 years ago by ★ 1.1k • written 5.5 years ago by ▴ 20
0
votes
4
replies
1.7k
views
Inconsistent geo_char for rse_tx
bug recount
6.3 years ago • updated 5.5 years ago Jacques.van-Helden • 0
0
votes
1
reply
1.1k
views
How to identify all SRPs with GTEx bigwig files?
recount
5.6 years ago hyp15 • 0
0
votes
2
replies
2.1k
views
Obtaining recount project data in TPM?
recount
updated 5.6 years ago by ★ 1.1k • written 5.7 years ago by • 0
3
votes
4
replies
1.8k
views
What assays are distributed with Recount TX data
recount recount2 RangedSummarizedExperiment
updated 5.6 years ago by ★ 1.1k • written 6.5 years ago by ▴ 120
1
vote
6
replies
2.0k
views
how to download bigwig from recount2?
recount
updated 5.7 years ago by 25k • written 5.7 years ago by • 0
1
vote
5
replies
2.0k
views
scale_counts targetSize normalization for recount2 counts
recount
updated 5.9 years ago by ★ 1.1k • written 5.9 years ago by • 0
0
votes
3
replies
2.3k
views
Problem constructing DESeq objects with large integers.
deseq2 recount
6.0 years ago Zach Brehm • 0
3
votes
3
replies
1.7k
views
Recount data for unannotated genes
recount RNAseq gencode lncRNA gene annotation
updated 6.0 years ago by ▴ 70 • written 6.1 years ago by ▴ 20
1
vote
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 6.0 years ago by ★ 1.1k • written 6.1 years ago by ▴ 20
0
votes
1
reply
3.9k
views
Is GTEx age and sex data available via the recount package?
recount gtex
updated 6.5 years ago by ★ 1.1k • written 6.5 years ago by • 0
0
votes
1
reply
1.3k
views
What does scaling RNASeq data using the area under coverage information (AUC) mean ? - related to recount package
library size factor recount
updated 6.6 years ago by ★ 1.1k • written 6.6 years ago by • 0
0
votes
3
replies
1.5k
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 7.1 years ago by ★ 1.1k • written 7.1 years ago by • 0
0
votes
2
replies
1.4k
views
Recount2 TCGA metadata missing sample, run and experiment columns
recount metadata tcga
updated 7.2 years ago by • 0 • written 7.2 years ago by • 0
3
votes
3
replies
2.2k
views
derfinder: how to merge regions and counts from individual chromosomes
derfinder recount
updated 7.4 years ago by ★ 1.1k • written 7.4 years ago by ▴ 510
0
votes
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 7.4 years ago by ★ 1.1k • written 7.5 years ago by • 0
0
votes
1
reply
3.5k
views
NA values of count matrix in class DESeqDataSet
rnaseq recount
7.6 years ago maleknias • 0
0
votes
1
reply
2.4k
views
Recount TCGA data
recount
updated 7.6 years ago by ★ 1.1k • written 7.6 years ago by • 0
0
votes
5
replies
2.7k
views
Matching columns to sample names
recount
updated 7.7 years ago by ★ 1.1k • written 7.7 years ago by • 0
2
votes
2
replies
1.7k
views
Number of IRanges elements in TCGA HiSeqV2 dataset
r tcga recount iranges
updated 7.9 years ago by ★ 1.1k • written 7.9 years ago by ▴ 20
3
votes
10
replies
2.4k
views
recount counts in the example experiment
recount
updated 7.9 years ago by ★ 1.1k • written 8.0 years ago by 43k
2
votes
1
reply
1.5k
views
recount not available
recount
updated 8.0 years ago by 25k • written 8.0 years ago by ★ 1.0k
2
votes
4
replies
2.6k
views
TCGA - Different Sample Number
recount
updated 8.1 years ago by ▴ 20 • written 8.1 years ago by • 0
0
votes
14
replies
4.0k
views
Error through importing (project = 'SRP009615') or even to download any BigWig File
recount Tutorial
updated 8.2 years ago by ★ 1.1k • written 8.2 years ago by • 0
1
vote
4
replies
3.3k
views
The recount package is not available for R version 3.3.1
recount
8.7 years ago arjunkrish • 0
38 results • Page 1 of 1
Recent ...
Replies
Comment: Differing results with DESeq2 by JKim • 0
My two cents. I think it would be more straightforward if you use cellmeans model. Have a look at [A guide to creating design matrices for …
Answer: CluserProfiler message "No gene can be mapped" by James W. MacDonald 68k
Your gene IDs are things like this: `Mpyr-NLJ1B.v3.hap1.scaffold1.g290550`, and the genes in your term2gene table are things like this: `Mp…
Answer: RNA-seq input to GRaNIE by James W. MacDonald 68k
This is [covered in the vignette.][1] [1]: https://bioconductor.org/packages/release/bioc/vignettes/GRaNIE/inst/doc/GRaNIE_packageDe…
Answer: Help using reduceSimMatrix with a custom annotation by sergisayolspuig ▴ 80
Hi there, `reduceSimMatrix()` expects a "GOALL" keytype in the OrgDb object when called with `children=TRUE` (which is the default for thi…
Answer: Analyzing TnSeq data with DESeq2 by cold.wolverine.arku • 0
That's a great use case of DESeq2! Even though it's not specifically tailored for TnSeq data, your approach to normalize and run explorator…
Votes
A: Unbalanced experiment with multiple samples from each patient.
A: Understanding contrasts limma
Answer: ROAST for small sets
Answer: ROAST for small sets
A: conceptual question about FDR, FDR adjusted p-value and q-value
Awards • All
Popular Question to Kinnary ▴ 20
Popular Question to sergisayolspuig ▴ 80
Popular Question to richardallenfriedmanbrooklyn ▴ 30
Scholar to Gordon Smyth 52k
Popular Question to shepherl 4.1k
Locations • All
United States, 19 minutes ago
United States, 1 hour ago
Brazil, 1 hour ago
United States, 1 hour ago
Switzerland, 1 hour ago
Traffic: 1097 users visited in the last hour
Content Search
Users
Tags
Badges
Help About
FAQ
Access RSS
API
Stats

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.

Powered by the version 2.3.6