Showing : recount • reset
1
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4
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1.4k
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NA values of count matrix in class DESeqDataSet
rna-seq recount
updated 4 months ago by ▴ 920 • written 4.0 years ago by • 0
0
votes
1
reply
212
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Using recount data to calculate Intron retention
snapcount recount3 recount
updated 5 months ago by ▴ 920 • written 5 months ago by • 0
0
votes
2
replies
269
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Recount2 Bigwigs for TCGA
R TCGA recount2 recount
updated 17 months ago by ▴ 920 • written 18 months ago by • 0
0
votes
1
reply
199
views
recount: inconsistency between pheno table structure for gene and transcript datasets
software error recount
updated 21 months ago by ▴ 920 • written 21 months ago by • 0
4
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7
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504
views
recount TCGA data one gene_id mapped to multiple symbols and vice versa
recount
updated 22 months ago by ▴ 920 • written 22 months ago by ▴ 20
0
votes
4
replies
475
views
Inconsistent geo_char for rse_tx
bug recount
2.7 years ago • updated 23 months ago Jacques.van-Helden • 0
0
votes
1
reply
211
views
How to identify all SRPs with GTEx bigwig files?
recount
2.0 years ago hyp15 • 0
0
votes
2
replies
549
views
Obtaining recount project data in TPM?
recount
updated 2.0 years ago by ▴ 920 • written 2.1 years ago by • 0
3
votes
4
replies
529
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What assays are distributed with Recount TX data
recount recount2 RangedSummarizedExperiment
updated 2.0 years ago by ▴ 920 • written 2.9 years ago by ▴ 100
1
vote
6
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542
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how to download bigwig from recount2?
recount
updated 2.1 years ago by 25k • written 2.1 years ago by • 0
1
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5
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503
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scale_counts targetSize normalization for recount2 counts
recount
updated 2.3 years ago by ▴ 920 • written 2.3 years ago by • 0
0
votes
3
replies
744
views
Problem constructing DESeq objects with large integers.
deseq2 recount
2.4 years ago • updated 2.3 years ago Zach Brehm • 0
3
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3
replies
482
views
Recount data for unannotated genes
recount RNAseq gencode lncRNA gene annotation
updated 2.4 years ago by ▴ 30 • written 2.5 years ago by ▴ 20
1
vote
1
reply
374
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Number of reads from recount are greater than target library size (40 million) for TCGA and GTEx projects
recount
updated 2.4 years ago by ▴ 920 • written 2.5 years ago by ▴ 20
0
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1
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1.5k
views
Is GTEx age and sex data available via the recount package?
recount gtex
updated 2.9 years ago by ▴ 920 • written 2.9 years ago by • 0
0
votes
1
reply
455
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What does scaling RNASeq data using the area under coverage information (AUC) mean ? - related to recount package
library size factor recount
updated 3.0 years ago by ▴ 920 • written 3.0 years ago by • 0
0
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3
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559
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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 3.5 years ago by ▴ 920 • written 3.5 years ago by • 0
0
votes
2
replies
491
views
Recount2 TCGA metadata missing sample, run and experiment columns
recount metadata tcga
updated 3.6 years ago by • 0 • written 3.6 years ago by • 0
3
votes
3
replies
823
views
derfinder: how to merge regions and counts from individual chromosomes
derfinder recount
updated 3.8 years ago by ▴ 920 • written 3.8 years ago by ▴ 480
0
votes
1
reply
601
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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 3.8 years ago by ▴ 920 • written 3.9 years ago by • 0
0
votes
1
reply
1.8k
views
NA values of count matrix in class DESeqDataSet
rnaseq recount
4.0 years ago maleknias • 0
0
votes
1
reply
1.1k
views
Recount TCGA data
recount
updated 4.0 years ago by ▴ 920 • written 4.0 years ago by • 0
0
votes
5
replies
857
views
Matching columns to sample names
recount
updated 4.1 years ago by ▴ 920 • written 4.1 years ago by • 0
2
votes
2
replies
773
views
Number of IRanges elements in TCGA HiSeqV2 dataset
r tcga recount iranges
updated 4.3 years ago by ▴ 920 • written 4.3 years ago by ▴ 20
3
votes
10
replies
1.0k
views
recount counts in the example experiment
recount
updated 4.3 years ago by ▴ 920 • written 4.4 years ago by 34k
2
votes
1
reply
685
views
recount not available
recount
updated 4.4 years ago by 25k • written 4.4 years ago by ★ 1.0k
2
votes
4
replies
1.2k
views
TCGA - Different Sample Number
recount
updated 4.5 years ago by ▴ 20 • written 4.5 years ago by • 0
0
votes
14
replies
1.7k
views
Error through importing (project = 'SRP009615') or even to download any BigWig File
recount Tutorial
updated 4.5 years ago by ▴ 920 • written 4.6 years ago by • 0
1
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4
replies
2.0k
views
The recount package is not available for R version 3.3.1
recount
5.1 years ago arjunkrish • 0
29 results • Page 1 of 1
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Comment: Diffbind dba.plotProfile attempt to select less than one element in OneIndex by bhanratt • 0
``` > DBA 10 Samples, 31953 sites in matrix: ID Tissue Factor Condition Replicate Reads FRiP 1 58 1 H3K4me3 AD …
Answer: Warning messages on Apple M1 BigSur by Vincent J. Carey, Jr. 6.5k
We are not producing M1 binaries at this time. If you use the intel version of R under Rosetta 2 you can use the intel mac binaries.
Comment: Issue::DesignPrimers DECIPHER by slwmartin • 0
Hey, I'm having this issue too. I've tried reinstalling using Conda a few times without luck. Did you reinstall with Conda or from the tar …
Comment: Log fold change interpretation of time series with Wald test by jd348 • 0
So would you recommend still using Log2fold change as a measurement for effect size?
Answer: Error in `*tmp*`$samples : $ operator is invalid for atomic vectors by James W. MacDonald 58k
I believe you want ``` > x <- as.matrix(read.delim("E:/bioinformatic/RNAseq/GSE168008_raw_count.txt", sep ="" ,row.names = 1)) > sampl…
Votes
Comment: Use of coef() as a measure of effect size in a multiple regression using DESeq2
Answer: Log fold change interpretation of time series with Wald test
A: gviz: name of tracks disappeas
Answer: Degust: what normalization method does it use
Answer: ylim and xlim in Enhanced Volcano
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