Showing : recount • reset
0
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2
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1.3k
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recount
recount
updated 15 months ago by ★ 1.1k • written 3.6 years ago by • 0
0
votes
1
reply
892
views
Recount3 error downloading data
recount3 recount
updated 18 months ago by ★ 1.1k • written 22 months ago by • 0
1
vote
1
reply
934
views
Transcript level expression for CCLE
recount3 recount CCLE
updated 22 months ago by ★ 1.1k • written 22 months ago by ▴ 510
2
votes
1
reply
970
views
Zero counts for all samples for all genes downloaded from recount3
recount
updated 2.3 years ago by ★ 5.0k • written 2.3 years ago by ▴ 10
0
votes
2
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1.4k
views
Recount3 data download problem
recount recount3
updated 2.6 years ago by ★ 1.1k • written 3.0 years ago by ▴ 10
2
votes
6
replies
2.2k
views
Unable to load data from duffel.rail
recount recountWorkflow recount3
updated 2.6 years ago by ★ 1.1k • written 3.0 years ago by • 0
0
votes
2
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1.3k
views
Cannot download data from IDIES links
recount recountWorkflow recount3
updated 2.6 years ago by ★ 1.1k • written 3.0 years ago by • 0
1
vote
3
replies
1.9k
views
Can i perform DEseq2 from 2 different rse objects download from RECOUNT database
DESeq2 recount GTEx TCGA recount3
updated 2.6 years ago by ★ 5.0k • written 2.6 years ago by ▴ 20
1
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1
reply
2.1k
views
recount3 - download bigwig files for TCGA data
recount3 recount TCGA
updated 3.7 years ago by ★ 1.1k • written 3.7 years ago by ▴ 10
1
vote
4
replies
5.1k
views
NA values of count matrix in class DESeqDataSet
rna-seq recount
updated 4.6 years ago by ★ 1.1k • written 8.2 years ago by • 0
0
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1
reply
1.7k
views
Using recount data to calculate Intron retention
snapcount recount3 recount
updated 4.7 years ago by ★ 1.1k • written 4.7 years ago by • 0
0
votes
2
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2.2k
views
Recount2 Bigwigs for TCGA
R TCGA recount2 recount
updated 5.7 years ago by ★ 1.1k • written 5.8 years ago by • 0
0
votes
1
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1.1k
views
recount: inconsistency between pheno table structure for gene and transcript datasets
software error recount
updated 6.0 years ago by ★ 1.1k • written 6.0 years ago by • 0
4
votes
7
replies
2.4k
views
recount TCGA data one gene_id mapped to multiple symbols and vice versa
recount
updated 6.1 years ago by ★ 1.1k • written 6.1 years ago by ▴ 20
0
votes
4
replies
1.9k
views
Inconsistent geo_char for rse_tx
bug recount
6.9 years ago • updated 6.1 years ago Jacques.van-Helden • 0
0
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1
reply
1.2k
views
How to identify all SRPs with GTEx bigwig files?
recount
6.3 years ago hyp15 • 0
0
votes
2
replies
2.4k
views
Obtaining recount project data in TPM?
recount
updated 6.3 years ago by ★ 1.1k • written 6.3 years ago by • 0
3
votes
4
replies
2.0k
views
What assays are distributed with Recount TX data
recount recount2 RangedSummarizedExperiment
updated 6.3 years ago by ★ 1.1k • written 7.1 years ago by ▴ 120
1
vote
6
replies
2.3k
views
how to download bigwig from recount2?
recount
updated 6.3 years ago by 25k • written 6.3 years ago by • 0
1
vote
5
replies
2.3k
views
scale_counts targetSize normalization for recount2 counts
recount
updated 6.5 years ago by ★ 1.1k • written 6.5 years ago by • 0
0
votes
3
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2.5k
views
Problem constructing DESeq objects with large integers.
deseq2 recount
6.6 years ago Zach Brehm • 0
3
votes
3
replies
2.0k
views
Recount data for unannotated genes
recount RNAseq gencode lncRNA gene annotation
updated 6.6 years ago by ▴ 70 • written 6.7 years ago by ▴ 20
1
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1
reply
1.4k
views
Number of reads from recount are greater than target library size (40 million) for TCGA and GTEx projects
recount
updated 6.7 years ago by ★ 1.1k • written 6.7 years ago by ▴ 20
0
votes
1
reply
4.2k
views
Is GTEx age and sex data available via the recount package?
recount gtex
updated 7.1 years ago by ★ 1.1k • written 7.1 years ago by • 0
0
votes
1
reply
1.5k
views
What does scaling RNASeq data using the area under coverage information (AUC) mean ? - related to recount package
library size factor recount
updated 7.2 years ago by ★ 1.1k • written 7.3 years ago by • 0
0
votes
3
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1.6k
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 7.7 years ago by ★ 1.1k • written 7.7 years ago by • 0
0
votes
2
replies
1.5k
views
Recount2 TCGA metadata missing sample, run and experiment columns
recount metadata tcga
updated 7.8 years ago by • 0 • written 7.8 years ago by • 0
3
votes
3
replies
2.4k
views
derfinder: how to merge regions and counts from individual chromosomes
derfinder recount
updated 8.0 years ago by ★ 1.1k • written 8.0 years ago by ▴ 510
0
votes
1
reply
1.6k
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 8.1 years ago by ★ 1.1k • written 8.1 years ago by • 0
0
votes
1
reply
3.7k
views
NA values of count matrix in class DESeqDataSet
rnaseq recount
8.2 years ago maleknias • 0
0
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1
reply
2.7k
views
Recount TCGA data
recount
updated 8.3 years ago by ★ 1.1k • written 8.3 years ago by • 0
0
votes
5
replies
3.1k
views
Matching columns to sample names
recount
updated 8.3 years ago by ★ 1.1k • written 8.3 years ago by • 0
2
votes
2
replies
1.9k
views
Number of IRanges elements in TCGA HiSeqV2 dataset
r tcga recount iranges
updated 8.5 years ago by ★ 1.1k • written 8.5 years ago by ▴ 20
3
votes
10
replies
2.7k
views
recount counts in the example experiment
recount
updated 8.6 years ago by ★ 1.1k • written 8.6 years ago by 43k
2
votes
1
reply
1.6k
views
recount not available
recount
updated 8.6 years ago by 25k • written 8.6 years ago by ★ 1.0k
2
votes
4
replies
2.8k
views
TCGA - Different Sample Number
recount
updated 8.8 years ago by ▴ 20 • written 8.8 years ago by • 0
0
votes
14
replies
4.5k
views
Error through importing (project = 'SRP009615') or even to download any BigWig File
recount Tutorial
updated 8.8 years ago by ★ 1.1k • written 8.8 years ago by • 0
1
vote
4
replies
3.5k
views
The recount package is not available for R version 3.3.1
recount
9.3 years ago arjunkrish • 0
38 results • Page 1 of 1
Recent ...
Replies
Comment: DECIPHER DesignProbes unable to design FISH-probes by Erik Wright ▴ 150
Are the sequences aligned (i.e., the same width) before running `TileSeqs()`?
Comment: BiocParallel (and DESeq2) - wrong args for environment subassignment by Michael Love 43k
BTW, I tested with no issue on MacOS ARM on our previous github issue.
Answer: DESeq(dds, parallel=TRUE) wrong args for environment subassignment by Michael Love 43k
The DESeq2 error makes sense, as we've talked about, given that the simple `bplapply` isn't working in your setup. Maybe give the traceb…
Answer: PTM analysis in LIMPA by Gordon Smyth 53k
For PTM analysis, the usual quantification command dpcQuant() is replaced by dpcImpute(). Otherwise the limpa pipeline is the same as for a…
Answer: problem reading bam files into nucleR by James W. MacDonald 68k
The first step is to update to the current versions of R/Bioconductor and try again. It's possible that you have run into a bug that's alre…
Votes
C: DESeq2 Following RSEM
Upcoming Ensembl API and data access changes - new blog post available
Comment: Highly similar RNA-seq samples in PCA - pooling or technical duplication?
Answer: Large logFC but somewhat high FDR
Comment: upstream git branches of bioc-release
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Popular Question to Hervé Pagès 16k
Popular Question to jared.andrews07 ▴ 30
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