Showing : recount • reset
0
votes
2
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1.1k
views
recount
recount
updated 4 months ago by ★ 1.1k • written 2.6 years ago by • 0
0
votes
1
reply
558
views
Recount3 error downloading data
recount3 recount
updated 6 months ago by ★ 1.1k • written 10 months ago by • 0
1
vote
1
reply
528
views
Transcript level expression for CCLE
recount3 recount CCLE
updated 10 months ago by ★ 1.1k • written 10 months ago by ▴ 510
2
votes
1
reply
711
views
Zero counts for all samples for all genes downloaded from recount3
recount
updated 16 months ago by ★ 4.6k • written 16 months ago by ▴ 10
0
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2
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1.1k
views
Recount3 data download problem
recount recount3
updated 19 months ago by ★ 1.1k • written 2.0 years ago by ▴ 10
2
votes
6
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1.7k
views
Unable to load data from duffel.rail
recount recountWorkflow recount3
updated 19 months ago by ★ 1.1k • written 2.0 years ago by • 0
0
votes
2
replies
987
views
Cannot download data from IDIES links
recount recountWorkflow recount3
updated 19 months ago by ★ 1.1k • written 24 months ago by • 0
1
vote
3
replies
1.5k
views
Can i perform DEseq2 from 2 different rse objects download from RECOUNT database
DESeq2 recount GTEx TCGA recount3
updated 19 months ago by ★ 4.6k • written 19 months ago by ▴ 20
1
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1
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1.5k
views
recount3 - download bigwig files for TCGA data
recount3 recount TCGA
updated 2.7 years ago by ★ 1.1k • written 2.7 years ago by ▴ 10
1
vote
4
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4.4k
views
NA values of count matrix in class DESeqDataSet
rna-seq recount
updated 3.7 years ago by ★ 1.1k • written 7.2 years ago by • 0
0
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1
reply
1.4k
views
Using recount data to calculate Intron retention
snapcount recount3 recount
updated 3.7 years ago by ★ 1.1k • written 3.7 years ago by • 0
0
votes
2
replies
1.7k
views
Recount2 Bigwigs for TCGA
R TCGA recount2 recount
updated 4.7 years ago by ★ 1.1k • written 4.8 years ago by • 0
0
votes
1
reply
896
views
recount: inconsistency between pheno table structure for gene and transcript datasets
software error recount
updated 5.0 years ago by ★ 1.1k • written 5.0 years ago by • 0
4
votes
7
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1.9k
views
recount TCGA data one gene_id mapped to multiple symbols and vice versa
recount
updated 5.1 years ago by ★ 1.1k • written 5.1 years ago by ▴ 20
0
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4
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1.6k
views
Inconsistent geo_char for rse_tx
bug recount
6.0 years ago • updated 5.2 years ago Jacques.van-Helden • 0
0
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1
reply
965
views
How to identify all SRPs with GTEx bigwig files?
recount
5.3 years ago hyp15 • 0
0
votes
2
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2.0k
views
Obtaining recount project data in TPM?
recount
updated 5.3 years ago by ★ 1.1k • written 5.3 years ago by • 0
3
votes
4
replies
1.7k
views
What assays are distributed with Recount TX data
recount recount2 RangedSummarizedExperiment
updated 5.3 years ago by ★ 1.1k • written 6.1 years ago by ▴ 120
1
vote
6
replies
1.8k
views
how to download bigwig from recount2?
recount
updated 5.4 years ago by 25k • written 5.4 years ago by • 0
1
vote
5
replies
1.8k
views
scale_counts targetSize normalization for recount2 counts
recount
updated 5.5 years ago by ★ 1.1k • written 5.5 years ago by • 0
0
votes
3
replies
2.2k
views
Problem constructing DESeq objects with large integers.
deseq2 recount
5.6 years ago Zach Brehm • 0
3
votes
3
replies
1.6k
views
Recount data for unannotated genes
recount RNAseq gencode lncRNA gene annotation
updated 5.7 years ago by ▴ 70 • written 5.7 years ago by ▴ 20
1
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1
reply
1.1k
views
Number of reads from recount are greater than target library size (40 million) for TCGA and GTEx projects
recount
updated 5.7 years ago by ★ 1.1k • written 5.7 years ago by ▴ 20
0
votes
1
reply
3.7k
views
Is GTEx age and sex data available via the recount package?
recount gtex
updated 6.2 years ago by ★ 1.1k • written 6.2 years ago by • 0
0
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1
reply
1.2k
views
What does scaling RNASeq data using the area under coverage information (AUC) mean ? - related to recount package
library size factor recount
updated 6.2 years ago by ★ 1.1k • written 6.3 years ago by • 0
0
votes
3
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1.4k
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 6.8 years ago by ★ 1.1k • written 6.8 years ago by • 0
0
votes
2
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1.3k
views
Recount2 TCGA metadata missing sample, run and experiment columns
recount metadata tcga
updated 6.8 years ago by • 0 • written 6.8 years ago by • 0
3
votes
3
replies
2.0k
views
derfinder: how to merge regions and counts from individual chromosomes
derfinder recount
updated 7.1 years ago by ★ 1.1k • written 7.1 years ago by ▴ 510
0
votes
1
reply
1.4k
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 7.1 years ago by ★ 1.1k • written 7.1 years ago by • 0
0
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1
reply
3.4k
views
NA values of count matrix in class DESeqDataSet
rnaseq recount
7.2 years ago maleknias • 0
0
votes
1
reply
2.3k
views
Recount TCGA data
recount
updated 7.3 years ago by ★ 1.1k • written 7.3 years ago by • 0
0
votes
5
replies
2.4k
views
Matching columns to sample names
recount
updated 7.3 years ago by ★ 1.1k • written 7.3 years ago by • 0
2
votes
2
replies
1.6k
views
Number of IRanges elements in TCGA HiSeqV2 dataset
r tcga recount iranges
updated 7.5 years ago by ★ 1.1k • written 7.5 years ago by ▴ 20
3
votes
10
replies
2.3k
views
recount counts in the example experiment
recount
updated 7.6 years ago by ★ 1.1k • written 7.6 years ago by 43k
2
votes
1
reply
1.4k
views
recount not available
recount
updated 7.7 years ago by 25k • written 7.7 years ago by ★ 1.0k
2
votes
4
replies
2.4k
views
TCGA - Different Sample Number
recount
updated 7.8 years ago by ▴ 20 • written 7.8 years ago by • 0
0
votes
14
replies
3.7k
views
Error through importing (project = 'SRP009615') or even to download any BigWig File
recount Tutorial
updated 7.8 years ago by ★ 1.1k • written 7.8 years ago by • 0
1
vote
4
replies
3.2k
views
The recount package is not available for R version 3.3.1
recount
8.3 years ago arjunkrish • 0
38 results • Page 1 of 1
Recent ...
Replies
Comment: Cross-validation with multiple control subgroups in limma by Ali Barry ▴ 40
Thanks so much for taking the time here, the insights are much appreciated. I suspected I'd have to ad hoc compare results if I did repeat …
Answer: Cross-validation with multiple control subgroups in limma by Gordon Smyth 52k
limma doesn't do cross-validation or resampling. Like most classical linear modeling procedures in statistics, limma uses a statistical mod…
Comment: Issues with seqlevelsStyle when making custom txdb objects for genomes/annotatio by Robert Castelo ★ 3.4k
Hi Hervé, thank you very much for your input into how to properly build and manage TxDb objects. gDNAx has two main inputs, one or more BAM…
Comment: Biostrings: Error writing long reads (>200 kbps) with writeQualityScaledXStringS by Aidan ▴ 60
Quick update: this is fixed in a branch awaiting PR to Biostrings (https://github.com/Bioconductor/Biostrings/pull/122). Should be in `deve…
Answer: Can DESeq2's design compensate for sequencing experimental design shortcomings? by Michael Love 43k
For statistical analysis plans, I recommend working with a local statistician or someone familiar with linear models in R. I have to reserv…
Votes
C: edgeR and lack of counts ID on CPM matrix
A: DESeq2 Following RSEM
A: importing RSEM data into DESeq2
A: Expected counts from RSEM in DESeq2
A: Using RSEM reads for DESeq2
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