Showing : recount • reset
0
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0
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175
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Recount3 error downloading data
recount3 recount
3 months ago Max Bone • 0
1
vote
1
reply
218
views
Transcript level expression for CCLE
recount3 recount CCLE
updated 3 months ago by ★ 1.0k • written 3 months ago by ▴ 510
2
votes
1
reply
474
views
Zero counts for all samples for all genes downloaded from recount3
recount
updated 9 months ago by ★ 4.1k • written 9 months ago by ▴ 10
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 ★ 4.1k • written 12 months ago by ▴ 20
0
votes
2
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698
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Cannot download data from IDIES links
recount recountWorkflow recount3
updated 12 months ago by ★ 1.0k • written 16 months ago by • 0
0
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2
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807
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Recount3 data download problem
recount recount3
updated 12 months ago by ★ 1.0k • written 17 months ago by • 0
2
votes
6
replies
1.3k
views
Unable to load data from duffel.rail
recount recountWorkflow recount3
updated 12 months ago by ★ 1.0k • written 17 months ago by • 0
0
votes
1
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723
views
recount
recount
updated 24 months ago by • 0 • written 24 months ago by • 0
1
vote
1
reply
1.1k
views
recount3 - download bigwig files for TCGA data
recount3 recount TCGA
updated 2.1 years ago by ★ 1.0k • written 2.1 years ago by ▴ 10
0
votes
1
reply
1.2k
views
Using recount data to calculate Intron retention
snapcount recount3 recount
updated 3.1 years ago by ★ 1.0k • written 3.1 years ago by • 0
0
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2
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1.4k
views
Recount2 Bigwigs for TCGA
R TCGA recount2 recount
updated 4.1 years ago by ★ 1.0k • written 4.2 years ago by • 0
0
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1
reply
745
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recount: inconsistency between pheno table structure for gene and transcript datasets
software error recount
updated 4.4 years ago by ★ 1.0k • written 4.4 years ago by • 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 ★ 1.0k • written 4.5 years ago by ▴ 20
0
votes
1
reply
793
views
How to identify all SRPs with GTEx bigwig files?
recount
4.7 years ago hyp15 • 0
0
votes
2
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1.7k
views
Obtaining recount project data in TPM?
recount
updated 4.7 years ago by ★ 1.0k • written 4.7 years ago by • 0
1
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6
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1.6k
views
how to download bigwig from recount2?
recount
updated 4.7 years ago by 25k • written 4.7 years ago by • 0
1
vote
5
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1.5k
views
scale_counts targetSize normalization for recount2 counts
recount
updated 4.9 years ago by ★ 1.0k • written 4.9 years ago by • 0
0
votes
3
replies
1.9k
views
Problem constructing DESeq objects with large integers.
deseq2 recount
5.0 years ago Zach Brehm • 0
1
vote
1
reply
956
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 ★ 1.0k • written 5.1 years ago by ▴ 20
3
votes
3
replies
1.3k
views
Recount data for unannotated genes
recount RNAseq gencode lncRNA gene annotation
updated 5.1 years ago by ▴ 70 • written 5.1 years ago by ▴ 20
0
votes
4
replies
1.3k
views
Inconsistent geo_char for rse_tx
bug recount
5.3 years ago • updated 4.6 years ago Jacques.van-Helden • 0
3
votes
4
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1.4k
views
What assays are distributed with Recount TX data
recount recount2 RangedSummarizedExperiment
updated 4.7 years ago by ★ 1.0k • written 5.5 years ago by ▴ 120
0
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1
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3.3k
views
Is GTEx age and sex data available via the recount package?
recount gtex
updated 5.5 years ago by ★ 1.0k • written 5.5 years ago by • 0
0
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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 ★ 1.0k • written 5.7 years ago by • 0
0
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3
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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 ★ 1.0k • written 6.1 years ago by • 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 • 0 • written 6.2 years ago by • 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 ★ 1.0k • written 6.4 years ago by ▴ 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 ★ 1.0k • written 6.5 years ago by • 0
0
votes
1
reply
3.0k
views
NA values of count matrix in class DESeqDataSet
rnaseq recount
6.6 years ago maleknias • 0
1
vote
4
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3.8k
views
NA values of count matrix in class DESeqDataSet
rna-seq recount
updated 3.0 years ago by ★ 1.0k • written 6.6 years ago by • 0
0
votes
1
reply
1.9k
views
Recount TCGA data
recount
updated 6.7 years ago by ★ 1.0k • written 6.7 years ago by • 0
0
votes
5
replies
1.9k
views
Matching columns to sample names
recount
updated 6.7 years ago by ★ 1.0k • written 6.7 years ago by • 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 ★ 1.0k • written 6.9 years ago by ▴ 20
3
votes
10
replies
2.0k
views
recount counts in the example experiment
recount
updated 7.0 years ago by ★ 1.0k • written 7.0 years ago by 41k
2
votes
1
reply
1.3k
views
recount not available
recount
updated 7.0 years ago by 25k • written 7.0 years ago by ★ 1.0k
2
votes
4
replies
2.1k
views
TCGA - Different Sample Number
recount
updated 7.2 years ago by ▴ 20 • written 7.2 years ago by • 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 ★ 1.0k • written 7.2 years ago by • 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: Help with running egsea() by Chris • 0
Thanks James! I update the question. The last question mean when we use `buildIdx()`, could we use gene symbol instead of entrezID. However…
Comment: Help with running egsea() by James W. MacDonald 65k
I don't understand the last question, but do look at the msigdb.gsets argument to `buildIdx` in the help page for that function.
Answer: Help with running egsea() by James W. MacDonald 65k
There are no arguments to `egsea.base`, as it is meant only as a helper function to return the different methods. In addition, if you are u…
Comment: How to use bootRanges to bootstrap small RNA loci (nullranges package) by Poonam • 0
I am working with mouse data. I don't know how to do this, but I will go through it. Can you help me with the second question? how do we …
Comment: [Mfuzz] Error in cmeans(exprs(eset) by Caio • 0
You can have this problem (lines with variance equal to zero) when you run experiments and obtain the data with more samples and use fewer …
Votes
Comment: Help with running egsea()
Answer: How to save the DEXSeq results
Answer: How to save the DEXSeq results
Answer: Help with running egsea()
Answer: Get genomic coordinates of CpGs sites (chromosomes, genomic position)
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