Showing : recount • reset
2
votes
6
replies
1.2k
views
Unable to load data from duffel.rail
recount recountWorkflow recount3
updated 11 months ago by ★ 1.0k • written 16 months 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
2
replies
1.1k
views
Recount2 TCGA metadata missing sample, run and experiment columns
recount metadata tcga
updated 6.1 years ago by • 0 • written 6.1 years ago by • 0
0
votes
2
replies
780
views
Recount3 data download problem
recount recount3
updated 11 months ago by ★ 1.0k • written 16 months ago by • 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 ▴ 70 • written 5.1 years ago by ▴ 20
0
votes
2
replies
667
views
Cannot download data from IDIES links
recount recountWorkflow recount3
updated 11 months ago by ★ 1.0k • written 16 months ago by • 0
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
1.9k
views
Recount TCGA data
recount
updated 6.6 years ago by ★ 1.0k • written 6.6 years ago by • 0
1
vote
4
replies
3.7k
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
1.2k
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 6.4 years ago by ★ 1.0k • written 6.4 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 ▴ 490
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 ★ 1.0k • written 6.1 years ago by • 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 ★ 1.0k • written 5.6 years ago by • 0
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 ★ 1.0k • written 5.5 years ago by • 0
3
votes
4
replies
1.4k
views
What assays are distributed with Recount TX data
recount recount2 RangedSummarizedExperiment
updated 4.6 years ago by ★ 1.0k • written 5.4 years ago by ▴ 120
1
vote
1
reply
937
views
Number of reads from recount are greater than target library size (40 million) for TCGA and GTEx projects
recount
updated 5.0 years ago by ★ 1.0k • written 5.1 years ago by ▴ 20
0
votes
3
replies
1.8k
views
Problem constructing DESeq objects with large integers.
deseq2 recount
4.9 years ago Zach Brehm • 0
1
vote
5
replies
1.5k
views
scale_counts targetSize normalization for recount2 counts
recount
updated 4.8 years ago by ★ 1.0k • written 4.9 years ago by • 0
1
vote
6
replies
1.6k
views
how to download bigwig from recount2?
recount
updated 4.7 years ago by 25k • written 4.7 years ago by • 0
0
votes
2
replies
1.6k
views
Obtaining recount project data in TPM?
recount
updated 4.6 years ago by ★ 1.0k • written 4.6 years ago by • 0
0
votes
1
reply
728
views
recount: inconsistency between pheno table structure for gene and transcript datasets
software error recount
updated 4.3 years ago by ★ 1.0k • written 4.4 years ago by • 0
0
votes
2
replies
1.4k
views
Recount2 Bigwigs for TCGA
R TCGA recount2 recount
updated 4.1 years ago by ★ 1.0k • written 4.1 years ago by • 0
0
votes
1
reply
1.1k
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
1
vote
1
reply
1.0k
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
1
vote
1
reply
192
views
Transcript level expression for CCLE
recount3 recount CCLE
updated 11 weeks ago by ★ 1.0k • written 11 weeks ago by ▴ 490
0
votes
14
replies
3.2k
views
Error through importing (project = 'SRP009615') or even to download any BigWig File
recount Tutorial
updated 7.1 years ago by ★ 1.0k • written 7.1 years ago by • 0
2
votes
4
replies
2.1k
views
TCGA - Different Sample Number
recount
updated 7.1 years ago by ▴ 20 • written 7.1 years ago by • 0
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
3
votes
10
replies
2.0k
views
recount counts in the example experiment
recount
updated 6.9 years ago by ★ 1.0k • written 6.9 years ago by 41k
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
0
votes
5
replies
1.9k
views
Matching columns to sample names
recount
updated 6.6 years ago by ★ 1.0k • written 6.6 years ago by • 0
2
votes
1
reply
456
views
Zero counts for all samples for all genes downloaded from recount3
recount
updated 8 months ago by ★ 4.0k • written 8 months ago by ▴ 10
1
vote
3
replies
976
views
Can i perform DEseq2 from 2 different rse objects download from RECOUNT database
DESeq2 recount GTEx TCGA recount3
updated 11 months ago by ★ 4.0k • written 11 months ago by ▴ 20
1
vote
4
replies
2.9k
views
The recount package is not available for R version 3.3.1
recount
7.7 years ago arjunkrish • 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
711
views
recount
recount
updated 23 months ago by • 0 • written 23 months ago by • 0
0
votes
1
reply
779
views
How to identify all SRPs with GTEx bigwig files?
recount
4.6 years ago hyp15 • 0
0
votes
0
replies
161
views
Recount3 error downloading data
recount3 recount
10 weeks ago Max Bone • 0
38 results • Page 1 of 1
Recent ...
Replies
Comment: Which input file is used for DGEList in EgdeR? by i.atanasoai • 0
Understood, Thank you very much for the reply, very kind.
Comment: Which input file is used for DGEList in EgdeR? by Michael Love 41k
"gene_counts_length_scaled.tsv file generated by the nf-core be exactly that?" No that is the counts scaled by the length. Counts + offset…
Comment: DESeq2 a lot of genes showing up as differentially expressed that only have 1 sa by Michael Love 41k
These genes are fine. They are just the ones where, by chance, the sample variance is below the sample mean. It happens. DESeq2 brings thes…
Comment: DEG with low counts by Michael Love 41k
These counts are too low, only a few samples above a count of 10. So for typical RNA-seq data that is underpowered to call differences. It…
Comment: DESeq filtering specific to contrasts by Michael Love 41k
If the counts are too low it in one group then you can't make the comparison either way (whether they are filtered out or just under-powere…
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A: Docker container with bioconductor and devtools
Answer: OrgDb for maize
Comment: significant difference of p-values with dream() after updating VariancePartition
How to tell and visualize up/down regulation of pathways from clusterprofiler gsea output
Comment: DEXSeq DEXSeqDataSet count matrix duplication
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