Showing : recount • reset
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1.3k
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recount
recount
updated 14 months ago by ★ 1.1k • written 3.5 years ago by • 0
0
votes
1
reply
861
views
Recount3 error downloading data
recount3 recount
updated 16 months ago by ★ 1.1k • written 20 months ago by • 0
1
vote
1
reply
883
views
Transcript level expression for CCLE
recount3 recount CCLE
updated 21 months ago by ★ 1.1k • written 21 months ago by ▴ 510
2
votes
1
reply
935
views
Zero counts for all samples for all genes downloaded from recount3
recount
updated 2.2 years ago by ★ 5.0k • written 2.2 years ago by ▴ 10
0
votes
2
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1.4k
views
Recount3 data download problem
recount recount3
updated 2.5 years ago by ★ 1.1k • written 2.9 years ago by ▴ 10
2
votes
6
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2.1k
views
Unable to load data from duffel.rail
recount recountWorkflow recount3
updated 2.5 years ago by ★ 1.1k • written 2.9 years ago by • 0
0
votes
2
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1.2k
views
Cannot download data from IDIES links
recount recountWorkflow recount3
updated 2.5 years ago by ★ 1.1k • written 2.8 years ago by • 0
1
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3
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1.8k
views
Can i perform DEseq2 from 2 different rse objects download from RECOUNT database
DESeq2 recount GTEx TCGA recount3
updated 2.5 years ago by ★ 5.0k • written 2.5 years ago by ▴ 20
1
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1
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2.0k
views
recount3 - download bigwig files for TCGA data
recount3 recount TCGA
updated 3.6 years ago by ★ 1.1k • written 3.6 years ago by ▴ 10
1
vote
4
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5.0k
views
NA values of count matrix in class DESeqDataSet
rna-seq recount
updated 4.5 years ago by ★ 1.1k • written 8.1 years ago by • 0
0
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1
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1.7k
views
Using recount data to calculate Intron retention
snapcount recount3 recount
updated 4.6 years ago by ★ 1.1k • written 4.6 years ago by • 0
0
votes
2
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2.1k
views
Recount2 Bigwigs for TCGA
R TCGA recount2 recount
updated 5.6 years ago by ★ 1.1k • written 5.6 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 5.9 years ago by ★ 1.1k • written 5.9 years ago by • 0
4
votes
7
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2.3k
views
recount TCGA data one gene_id mapped to multiple symbols and vice versa
recount
updated 6.0 years ago by ★ 1.1k • written 6.0 years ago by ▴ 20
0
votes
4
replies
1.9k
views
Inconsistent geo_char for rse_tx
bug recount
6.8 years ago • updated 6.0 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
6.1 years ago hyp15 • 0
0
votes
2
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2.3k
views
Obtaining recount project data in TPM?
recount
updated 6.1 years ago by ★ 1.1k • written 6.2 years ago by • 0
3
votes
4
replies
2.0k
views
What assays are distributed with Recount TX data
recount recount2 RangedSummarizedExperiment
updated 6.1 years ago by ★ 1.1k • written 7.0 years ago by ▴ 120
1
vote
6
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2.3k
views
how to download bigwig from recount2?
recount
updated 6.2 years ago by 25k • written 6.2 years ago by • 0
1
vote
5
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2.3k
views
scale_counts targetSize normalization for recount2 counts
recount
updated 6.4 years ago by ★ 1.1k • written 6.4 years ago by • 0
0
votes
3
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2.4k
views
Problem constructing DESeq objects with large integers.
deseq2 recount
6.5 years ago Zach Brehm • 0
3
votes
3
replies
1.9k
views
Recount data for unannotated genes
recount RNAseq gencode lncRNA gene annotation
updated 6.5 years ago by ▴ 70 • written 6.6 years ago by ▴ 20
1
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1
reply
1.3k
views
Number of reads from recount are greater than target library size (40 million) for TCGA and GTEx projects
recount
updated 6.5 years ago by ★ 1.1k • written 6.6 years ago by ▴ 20
0
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1
reply
4.1k
views
Is GTEx age and sex data available via the recount package?
recount gtex
updated 7.0 years ago by ★ 1.1k • written 7.0 years ago by • 0
0
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1
reply
1.4k
views
What does scaling RNASeq data using the area under coverage information (AUC) mean ? - related to recount package
library size factor recount
updated 7.1 years ago by ★ 1.1k • written 7.2 years ago by • 0
0
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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 7.6 years ago by ★ 1.1k • written 7.6 years ago by • 0
0
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2
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1.5k
views
Recount2 TCGA metadata missing sample, run and experiment columns
recount metadata tcga
updated 7.7 years ago by • 0 • written 7.7 years ago by • 0
3
votes
3
replies
2.4k
views
derfinder: how to merge regions and counts from individual chromosomes
derfinder recount
updated 7.9 years ago by ★ 1.1k • written 7.9 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 8.0 years ago by ★ 1.1k • written 8.0 years ago by • 0
0
votes
1
reply
3.6k
views
NA values of count matrix in class DESeqDataSet
rnaseq recount
8.1 years ago maleknias • 0
0
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1
reply
2.6k
views
Recount TCGA data
recount
updated 8.1 years ago by ★ 1.1k • written 8.1 years ago by • 0
0
votes
5
replies
3.0k
views
Matching columns to sample names
recount
updated 8.2 years ago by ★ 1.1k • written 8.2 years ago by • 0
2
votes
2
replies
1.8k
views
Number of IRanges elements in TCGA HiSeqV2 dataset
r tcga recount iranges
updated 8.4 years ago by ★ 1.1k • written 8.4 years ago by ▴ 20
3
votes
10
replies
2.6k
views
recount counts in the example experiment
recount
updated 8.5 years ago by ★ 1.1k • written 8.5 years ago by 43k
2
votes
1
reply
1.6k
views
recount not available
recount
updated 8.5 years ago by 25k • written 8.5 years ago by ★ 1.0k
2
votes
4
replies
2.8k
views
TCGA - Different Sample Number
recount
updated 8.6 years ago by ▴ 20 • written 8.6 years ago by • 0
0
votes
14
replies
4.4k
views
Error through importing (project = 'SRP009615') or even to download any BigWig File
recount Tutorial
updated 8.7 years ago by ★ 1.1k • written 8.7 years ago by • 0
1
vote
4
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3.4k
views
The recount package is not available for R version 3.3.1
recount
9.2 years ago arjunkrish • 0
38 results • Page 1 of 1
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Comment: Best practice for handling large data (matrix with >2^31-1 non-zero elements) in by James W. MacDonald 68k
Aaron already answered your question. If you have an HDF5 file, it will be read in as a `TENxMatrix` object, which isn't actually read in -…
Comment: Best practice for handling large data (matrix with >2^31-1 non-zero elements) in by dan.gatti • 0
Very strange. We have the same package versions. I tried adding the mtx.class, type, and delayed arguments, but it's still making the coun…
Comment: DESeq2 for candidate gene analysis by piffelpaff ▴ 20
thank you so much for answering Dr. Love!
Answer: DESeq2 for candidate gene analysis by Michael Love 43k
Your plan 1 is reasonable. Run DESeq2 on the whole dataset to obtain size factors and moderated dispersion estimates and then extract the u…
Comment: Best practice for handling large data (matrix with >2^31-1 non-zero elements) in by James W. MacDonald 68k
Oh. ``` > z <- read10xCounts(c(tmpdir, tmpdir), mtx.class = "SVT_SparseMatrix", delayed = TRUE) > class(counts(z)) [1] "DelayedMatrix" att…
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A: Multi-level experiments in Limma
Answer: Should voomWithQualityWeights still be used when the sample-specific weights var
Answer: DESeq2 for candidate gene analysis
DESeq2 for candidate gene analysis
Answer: DESeq2 for candidate gene analysis
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