Showing : recount • reset
0
votes
2
replies
300
views
Recount3 data download problem
recount recount3
updated 28 days ago by ★ 1.0k • written 5 months ago by • 0
2
votes
6
replies
577
views
Unable to load data from duffel.rail
recount recountWorkflow recount3
updated 28 days ago by ★ 1.0k • written 5 months ago by • 0
0
votes
2
replies
302
views
Cannot download data from IDIES links
recount recountWorkflow recount3
updated 28 days ago by ★ 1.0k • written 5 months ago by • 0
0
votes
3
replies
269
views
Can i perform DEseq2 from 2 different rse objects download from RECOUNT database
DESeq2 recount GTEx TCGA recount3
updated 4 weeks ago by ★ 2.9k • written 4 weeks ago by ▴ 20
0
votes
1
reply
378
views
recount
recount
updated 13 months ago by • 0 • written 13 months ago by • 0
1
vote
1
reply
609
views
recount3 - download bigwig files for TCGA data
recount3 recount TCGA
updated 14 months ago by ★ 1.0k • written 14 months ago by ▴ 10
1
vote
4
replies
2.7k
views
NA values of count matrix in class DESeqDataSet
rna-seq recount
updated 2.1 years ago by ★ 1.0k • written 5.7 years ago by • 0
0
votes
1
reply
805
views
Using recount data to calculate Intron retention
snapcount recount3 recount
updated 2.2 years ago by ★ 1.0k • written 2.2 years ago by • 0
0
votes
2
replies
957
views
Recount2 Bigwigs for TCGA
R TCGA recount2 recount
updated 3.2 years ago by ★ 1.0k • written 3.2 years ago by • 0
0
votes
1
reply
455
views
recount: inconsistency between pheno table structure for gene and transcript datasets
software error recount
updated 3.5 years ago by ★ 1.0k • written 3.5 years ago by • 0
4
votes
7
replies
1.1k
views
recount TCGA data one gene_id mapped to multiple symbols and vice versa
recount
updated 3.6 years ago by ★ 1.0k • written 3.6 years ago by ▴ 20
0
votes
4
replies
913
views
Inconsistent geo_char for rse_tx
bug recount
4.4 years ago • updated 3.6 years ago Jacques.van-Helden • 0
0
votes
1
reply
524
views
How to identify all SRPs with GTEx bigwig files?
recount
3.7 years ago hyp15 • 0
0
votes
2
replies
1.2k
views
Obtaining recount project data in TPM?
recount
updated 3.8 years ago by ★ 1.0k • written 3.8 years ago by • 0
3
votes
4
replies
1.0k
views
What assays are distributed with Recount TX data
recount recount2 RangedSummarizedExperiment
updated 3.8 years ago by ★ 1.0k • written 4.6 years ago by ▴ 120
1
vote
6
replies
1.1k
views
how to download bigwig from recount2?
recount
updated 3.8 years ago by 25k • written 3.8 years ago by • 0
1
vote
5
replies
1.1k
views
scale_counts targetSize normalization for recount2 counts
recount
updated 4.0 years ago by ★ 1.0k • written 4.0 years ago by • 0
0
votes
3
replies
1.4k
views
Problem constructing DESeq objects with large integers.
deseq2 recount
4.1 years ago Zach Brehm • 0
3
votes
3
replies
948
views
Recount data for unannotated genes
recount RNAseq gencode lncRNA gene annotation
updated 4.1 years ago by ▴ 70 • written 4.2 years ago by ▴ 20
1
vote
1
reply
676
views
Number of reads from recount are greater than target library size (40 million) for TCGA and GTEx projects
recount
updated 4.1 years ago by ★ 1.0k • written 4.2 years ago by ▴ 20
0
votes
1
reply
2.5k
views
Is GTEx age and sex data available via the recount package?
recount gtex
updated 4.6 years ago by ★ 1.0k • written 4.6 years ago by • 0
0
votes
1
reply
786
views
What does scaling RNASeq data using the area under coverage information (AUC) mean ? - related to recount package
library size factor recount
updated 4.7 years ago by ★ 1.0k • written 4.8 years ago by • 0
0
votes
3
replies
866
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 5.2 years ago by ★ 1.0k • written 5.2 years ago by • 0
0
votes
2
replies
770
views
Recount2 TCGA metadata missing sample, run and experiment columns
recount metadata tcga
updated 5.3 years ago by • 0 • written 5.3 years ago by • 0
3
votes
3
replies
1.3k
views
derfinder: how to merge regions and counts from individual chromosomes
derfinder recount
updated 5.5 years ago by ★ 1.0k • written 5.5 years ago by ▴ 490
0
votes
1
reply
894
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 5.6 years ago by ★ 1.0k • written 5.6 years ago by • 0
0
votes
1
reply
2.6k
views
NA values of count matrix in class DESeqDataSet
rnaseq recount
5.7 years ago maleknias • 0
0
votes
1
reply
1.6k
views
Recount TCGA data
recount
updated 5.7 years ago by ★ 1.0k • written 5.7 years ago by • 0
0
votes
5
replies
1.4k
views
Matching columns to sample names
recount
updated 5.8 years ago by ★ 1.0k • written 5.8 years ago by • 0
2
votes
2
replies
1.1k
views
Number of IRanges elements in TCGA HiSeqV2 dataset
r tcga recount iranges
updated 6.0 years ago by ★ 1.0k • written 6.0 years ago by ▴ 20
3
votes
10
replies
1.5k
views
recount counts in the example experiment
recount
updated 6.1 years ago by ★ 1.0k • written 6.1 years ago by 40k
2
votes
1
reply
954
views
recount not available
recount
updated 6.1 years ago by 25k • written 6.1 years ago by ★ 1.0k
2
votes
4
replies
1.8k
views
TCGA - Different Sample Number
recount
updated 6.2 years ago by ▴ 20 • written 6.2 years ago by • 0
0
votes
14
replies
2.5k
views
Error through importing (project = 'SRP009615') or even to download any BigWig File
recount Tutorial
updated 6.3 years ago by ★ 1.0k • written 6.3 years ago by • 0
1
vote
4
replies
2.5k
views
The recount package is not available for R version 3.3.1
recount
6.8 years ago arjunkrish • 0
35 results • Page 1 of 1
Recent ...
Replies
Answer: DESeq2 + analysis question for design with uneven time point design by Michael Love 40k
I'd recommend reaching out to a local statistician or someone familiar with linear models in R. Unfortunately, I have to reserve my time on…
Answer: Genes with highest differential expression have very low read counts for most ge by Michael Love 40k
Have you use `lfcShrink`? Or `results` with `lfcThreshold`? Either of these are recommended for prioritizing DE genes.
Comment: Adjusting for baseline when having longitudinal data, mixed model and no treat by Gordon Smyth 47k
> equivqalent in limma would be like a gene by gene specificic design matrix where no BL time point would exist but a continuous variable t…
Comment: Extract Limma Adjusted Values for Plotting by ATpoint ★ 2.9k
Yes, with normalized counts on log2 scale.
Comment: Adjusting for baseline when having longitudinal data, mixed model and no treat by Anna ▴ 20
A no I never referred to transcriptomic data when I was talking about "standard procedure" I was referring to the way we analyze longitudin…
Votes
A: Ranges from a fasta file
Answer: NA transcript values in my Txdb
Comment: Interpret plot from DiffBind
Answer: Use with_go along with other filters in getBM function
Answer: Use with_go along with other filters in getBM function
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