Showing : recount • reset
0
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0
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166
views
Recount3 error downloading data
recount3 recount
11 weeks ago Max Bone • 0
1
vote
1
reply
196
views
Transcript level expression for CCLE
recount3 recount CCLE
updated 12 weeks ago by ★ 1.0k • written 12 weeks ago by ▴ 490
2
votes
1
reply
461
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
0
votes
2
replies
786
views
Recount3 data download problem
recount recount3
updated 11 months ago by ★ 1.0k • written 16 months ago by • 0
2
votes
6
replies
1.3k
views
Unable to load data from duffel.rail
recount recountWorkflow recount3
updated 11 months ago by ★ 1.0k • written 16 months ago by • 0
0
votes
2
replies
676
views
Cannot download data from IDIES links
recount recountWorkflow recount3
updated 11 months ago by ★ 1.0k • written 16 months ago by • 0
1
vote
3
replies
998
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
0
votes
1
reply
713
views
recount
recount
updated 23 months ago by • 0 • written 23 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
1
vote
4
replies
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
1.2k
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 4.1 years ago by • 0
0
votes
1
reply
733
views
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
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
784
views
How to identify all SRPs with GTEx bigwig files?
recount
4.6 years ago hyp15 • 0
0
votes
2
replies
1.6k
views
Obtaining recount project data in TPM?
recount
updated 4.6 years ago by ★ 1.0k • written 4.7 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 5.5 years ago by ▴ 120
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
1
vote
5
replies
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
1.8k
views
Problem constructing DESeq objects with large integers.
deseq2 recount
5.0 years ago Zach Brehm • 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
1
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1
reply
947
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
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
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 5.7 years ago by • 0
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
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 ▴ 490
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 6.5 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
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
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 6.9 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 7.1 years ago by ▴ 20 • written 7.1 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
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Comment: Reproducibility issue with scran together with lapply and BiocParallel by ATpoint ★ 4.0k
Thanks Aaron for the response. RNGseed (for me) has no effect. I actually stumbled over this in one of my analysis where I have a constant …
Comment: Opposite sign of LFC in count plots of DEGs (DESeq2) by winwater0928 • 0
Thank you for your comment! 1)"Your contrast is comparing LGR5 to Homeostasis." means (Lgr5)/(Homeostasis). Is it right? Then, I think if…
Answer: Reproducibility issue with scran together with lapply and BiocParallel by Aaron Lun ★ 28k
IIRC **BiocParallel** switches to a different RNG when inside its own functions like `bplapply` - specifically L'Ecuyer-CMRG, as opposed to…
Comment: DESeq2 output used for PCA plot on R studio by swbarnes2 ★ 1.3k
This looks terrible for RNASeq data, because it's not RNASeq data. It's a matrix of pretty random numbers, which you know because you poste…
Comment: DESeq2 output used for PCA plot on R studio by Aaliya • 0
I had taken this code from internet, but after reading about it and I did on my own, I would be making a post to ask for the suggestions if…
Votes
C: null model and DEXSeqDataSet object in DEXSEQ
A: Are published RNA seq data analyses often wrong in calculating p-values and FDR?
A: How to explain how DESeq2 works to someone with zero bioinformatics background?
Answer: Interpret plot from DiffBind
Answer: How to retrieve gene ontology GO class from gene list?
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