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Showing :
easyRNASeq
•
reset
0
votes
17
replies
2.8k
views
Issue with easyRNASeq
easyRNASeq
error
8.8 years ago
ea11g0
• 0
1
vote
13
replies
3.0k
views
Several issues with the package easyRNASeq
easyrnaseq
bug
8.9 years ago • updated 8.8 years ago
Michael Dondrup
▴ 10
0
votes
8
replies
2.0k
views
Using easyRNASeq package: question about BAM/BAI and links to them
easyRNASeq
easyRNASeq
updated 10.5 years ago by
Sylvain Foisy
▴ 80 • written 10.5 years ago by
Sylvain Foisy
▴ 80
0
votes
7
replies
2.6k
views
GTF file error when using easyRNAseq�
Annotation
Organism
BSgenome
BSgenome
DESeq
easyRNASeq
Annotation
Organism
BSgenome
DESeq
updated 10.5 years ago by
delhomme@embl.de
★ 1.2k • written 10.5 years ago by
Guest User
★ 13k
0
votes
7
replies
2.2k
views
Getting counts for previously undetected transcripts and genes with easyRNASeq: comparison to Cufflinks
RNASeq
Annotation
Cancer
edgeR
cqn
easyRNASeq
RNASeq
Annotation
Cancer
edgeR
cqn
updated 11.4 years ago by
delhomme@embl.de
★ 1.2k • written 11.4 years ago by
Richard Friedman
★ 2.0k
2
votes
6
replies
2.0k
views
easyRNAseq says Your annotation is not in sync with your alignments!
easyRNAseq
updated 9.2 years ago by
Nicolas Delhomme
▴ 320 • written 9.3 years ago by
Mayte
• 0
0
votes
6
replies
1.3k
views
question on easyRNASeq developer version
easyRNASeq
easyRNASeq
updated 11.6 years ago by
RenéBöttcher
▴ 20 • written 11.6 years ago by
delhomme@embl.de
★ 1.2k
0
votes
6
replies
1.7k
views
easyRNASeq: "Error in IRangesList"
easyRNASeq
8.9 years ago
surjray
• 0
0
votes
5
replies
2.3k
views
easyRNAseq annotation file
easyrnaseq
annotation
8.7 years ago • updated 8.6 years ago
kylvalda
• 0
0
votes
5
replies
1.6k
views
EasyRNAseq - error in building count table - Error in unlist
Sequencing
RNASeq
edgeR
easyRNASeq
Sequencing
RNASeq
edgeR
easyRNASeq
updated 10.7 years ago by
delhomme@embl.de
★ 1.2k • written 10.7 years ago by
Guest User
★ 13k
0
votes
5
replies
2.6k
views
count tables created with easyRNASeq and the rpkm() function from edgeR
easyrnaseq
edger
rpkm
updated 9.2 years ago by
Nicolas Delhomme
▴ 320 • written 9.2 years ago by
Sylvain Foisy
▴ 80
1
vote
5
replies
2.1k
views
Getting a count matrix from a SummerizedExpriment with EasyRNASeq
easyrnaseq
9.5 years ago
Sylvain Foisy
▴ 80
4
votes
5
replies
1.4k
views
Warning: missing reverse strand option in easyRNASeq.
easyrnaseq
rnaseq
strand
updated 6.9 years ago by
Hervé Pagès
16k • written 6.9 years ago by
Michael Dondrup
▴ 10
0
votes
5
replies
2.4k
views
EasyRNASeq issue (missing bai files)
GO
PROcess
DESeq
easyRNASeq
GO
PROcess
DESeq
easyRNASeq
updated 11.8 years ago by
Jorge Beira
▴ 10 • written 11.8 years ago by
delhomme@embl.de
★ 1.2k
0
votes
4
replies
1.7k
views
easyRNASeq error
Sequencing
Alignment
Annotation
Organism
BSgenome
biomaRt
BSgenome
easyRNASeq
Sequencing
12.2 years ago
delhomme@embl.de
★ 1.2k
0
votes
4
replies
1.1k
views
easyRNAseq question
easyRNASeq
easyRNASeq
updated 12.0 years ago by
Akula, Nirmala NIH/NIMH [C]
▴ 190 • written 12.0 years ago by
delhomme@embl.de
★ 1.2k
0
votes
3
replies
1.9k
views
Error: 'devel' version requires a more recent R
GUI
Cancer
easyRNASeq
GUI
Cancer
easyRNASeq
updated 11.5 years ago by
Sean Davis
21k • written 11.5 years ago by
Richard Friedman
★ 2.0k
0
votes
3
replies
1.2k
views
simpleRNASeq easyRNAseq warnings edgeR error
simplernaseq
easyrnaseq
edger
DEformats
updated 6.2 years ago by
Nicolas Delhomme
▴ 320 • written 6.3 years ago by
KGies
• 0
0
votes
2
replies
1.1k
views
easyRNASeq package: error when summarizing per gene
RNASeq
Annotation
Organism
BSgenome
BSgenome
easyRNASeq
RNASeq
Annotation
Organism
updated 11.6 years ago by
delhomme@embl.de
★ 1.2k • written 11.6 years ago by
Guest User
★ 13k
0
votes
2
replies
1.0k
views
easyRNAseq question
Category
DESeq
easyRNASeq
Category
DESeq
easyRNASeq
updated 11.8 years ago by
Wolfgang Huber
★ 13k • written 11.9 years ago by
Akula, Nirmala NIH/NIMH [C]
▴ 190
0
votes
2
replies
1.3k
views
easyRNASeq install problem
easyRNASeq
easyRNASeq
updated 11.8 years ago by
Sean Davis
21k • written 11.8 years ago by
Loraine, Ann
▴ 50
0
votes
2
replies
2.5k
views
counting RNA-seq reads in R/BioC
GO
Infrastructure
Rsubread
easyRNASeq
GO
Infrastructure
Rsubread
easyRNASeq
updated 11.7 years ago by
Valerie Obenchain
★ 6.8k • written 11.7 years ago by
Mark Robinson
▴ 880
0
votes
2
replies
1.3k
views
Error of GTF Annotation in easyRNASeq
miRNA
Annotation
easyRNASeq
miRNA
Annotation
easyRNASeq
11.6 years ago
delhomme@embl.de
★ 1.2k
0
votes
2
replies
1.0k
views
RNAseq object
RNASeq
DESeq
easyRNASeq
RNASeq
DESeq
easyRNASeq
updated 11.6 years ago by
Tim Triche
★ 4.2k • written 11.6 years ago by
Guest User
★ 13k
0
votes
2
replies
1.3k
views
error message with easyRNASeq use case
RNASeq
Cancer
Organism
easyRNASeq
RNASeq
Cancer
Organism
easyRNASeq
updated 11.4 years ago by
James W. MacDonald
65k • written 11.4 years ago by
Richard Friedman
★ 2.0k
0
votes
2
replies
2.2k
views
using easyRNASeq to calculate RPKM values
easyRNASeq
easyRNASeq
updated 11.3 years ago by
delhomme@embl.de
★ 1.2k • written 11.3 years ago by
Fatemehsadat Seyednasrollah
▴ 260
0
votes
2
replies
1.3k
views
Devel version of easyRNASeq: using the simpleRNASeq method gives an error
Annotation
easyRNASeq
Annotation
easyRNASeq
updated 10.1 years ago by
Sylvain Foisy
▴ 80 • written 10.1 years ago by
Nicolas Delhomme
▴ 320
0
votes
2
replies
1.5k
views
easyRNAseq and DEseq for no replicate RNAseq
RNASeq
PROcess
easyRNASeq
RNASeq
PROcess
easyRNASeq
updated 10.4 years ago by
Nicolas Delhomme
▴ 320 • written 10.5 years ago by
Isabelle Stévant
▴ 10
0
votes
2
replies
1.3k
views
simpleRNASeq error importing BAM files
simpleRNASeq
easyRNASeq
updated 8.9 years ago by
James W. MacDonald
65k • written 8.9 years ago by
ea11g0
• 0
2
votes
2
replies
1.4k
views
Error reading BAM file with duplicated header in easyRNAseq and GenomicAlignments
software error
easyrnaseq
genomicalignments
bam
updated 8.6 years ago by
Martin Morgan
25k • written 8.6 years ago by
Michael Dondrup
▴ 10
0
votes
2
replies
1.6k
views
Package installation errors for Bioconductor and easyRNASeq
installation
biocinstaller
easyrnaseq
updated 8.4 years ago by
Martin Morgan
25k • written 8.4 years ago by
michael.dhar
• 0
1
vote
2
replies
2.3k
views
mgcv not updating
mgcv
easyRNASeq
updated 3.2 years ago by
Martin Morgan
25k • written 3.2 years ago by
Aliza
▴ 10
0
votes
1
reply
1.9k
views
Using a countDataSet as input data in DESeq2
easyRNASeq
easyRNASeq
updated 10.4 years ago by
Michael Love
42k • written 10.4 years ago by
Guest User
★ 13k
0
votes
1
reply
1.4k
views
Problems in running easyRNASeq
Annotation
Organism
DEGseq
easyRNASeq
Annotation
Organism
DEGseq
easyRNASeq
updated 11.3 years ago by
delhomme@embl.de
★ 1.2k • written 11.3 years ago by
Guest User
★ 13k
0
votes
1
reply
1.1k
views
it is strange that I cannot get the fpkm by using easyRNASeq
Annotation
BSgenome
BSgenome
easyRNASeq
Annotation
BSgenome
BSgenome
easyRNASeq
updated 11.1 years ago by
Nicolas Delhomme
▴ 30 • written 11.1 years ago by
Guest User
★ 13k
0
votes
1
reply
1.4k
views
easyRNASeq packages: overlapping exons warning unsolved (?) and use of paired end information
Coverage
Annotation
GO
Cancer
Organism
edgeR
DESeq
GenomicRanges
Rsubread
easyRNASeq
GO
updated 10.4 years ago by
Nicolas Delhomme
▴ 320 • written 10.4 years ago by
Gordon Smyth
50k
0
votes
1
reply
1.4k
views
eayRNASeq with Ensemble GRCh37 help
Annotation
Organism
easyRNASeq
DESeq2
Annotation
Organism
easyRNASeq
DESeq2
updated 10.6 years ago by
delhomme@embl.de
★ 1.2k • written 10.6 years ago by
Aki Hoji
▴ 10
0
votes
1
reply
860
views
warnings on easyRNASeq package
Annotation
Organism
PROcess
GenomicRanges
easyRNASeq
Annotation
Organism
PROcess
updated 11.6 years ago by
Mun Hua Tan
▴ 10 • written 11.6 years ago by
delhomme@embl.de
★ 1.2k
0
votes
1
reply
1.2k
views
Devel version of easyRNASeq: using the simpleRNASeq method gives an error
easyRNASeq
easyRNASeq
updated 10.1 years ago by
Nicolas Delhomme
▴ 320 • written 10.1 years ago by
Sylvain Foisy
▴ 80
0
votes
1
reply
892
views
Regarding an issue with easyRNASeq - from Surjyendu Ray.
Organism
edgeR
easyRNASeq
Organism
edgeR
easyRNASeq
11.7 years ago
delhomme@embl.de
★ 1.2k
0
votes
1
reply
3.2k
views
easyRNASeq error: Error in aggregate.data.frame(as.data.frame(x), ...) : no rows to aggregate
easyrnaseq
9.5 years ago
sylvian
• 0
0
votes
1
reply
1.3k
views
Warnings with running easyRNASeq with easyRNASeq tutorial
RNASeq
Annotation
GUI
Cancer
BSgenome
BSgenome
easyRNASeq
RNASeq
Annotation
GUI
Cancer
updated 11.8 years ago by
delhomme@embl.de
★ 1.2k • written 11.8 years ago by
Richard Friedman
★ 2.0k
0
votes
1
reply
810
views
Problems easyRNASeq
Annotation
PROcess
easyRNASeq
Annotation
PROcess
easyRNASeq
updated 12.1 years ago by
delhomme@embl.de
★ 1.2k • written 12.1 years ago by
Yates, Steven A
▴ 10
0
votes
1
reply
1.4k
views
simpleRNASeq stopped running (related to S4 vectors?)
simplernaseq
easyrnaseq
s4vectors
updated 8.4 years ago by
Nicolas Delhomme
▴ 320 • written 8.4 years ago by
michael.dhar
• 0
0
votes
1
reply
1.0k
views
How to combine different annotation (chromosomic, genic) when using easyRNASeq (was easyRNASeq error)
RNASeq
Annotation
Organism
biomaRt
easyRNASeq
RNASeq
Annotation
Organism
biomaRt
updated 12.2 years ago by
Davis, Wade
▴ 350 • written 12.2 years ago by
delhomme@embl.de
★ 1.2k
0
votes
1
reply
1.4k
views
error in easyRNASeq
RNASeq
BSgenome
BSgenome
easyRNASeq
RNASeq
BSgenome
BSgenome
easyRNASeq
updated 11.5 years ago by
delhomme@embl.de
★ 1.2k • written 11.5 years ago by
Mayte Suarez-Farinas
▴ 510
0
votes
1
reply
1.0k
views
easyRNASeq and edgeR
BSgenome
BSgenome
edgeR
easyRNASeq
BSgenome
BSgenome
edgeR
easyRNASeq
updated 11.5 years ago by
delhomme@embl.de
★ 1.2k • written 11.5 years ago by
Guest User
★ 13k
0
votes
1
reply
858
views
bam files in sub-directories
easyRNASeq
easyRNASeq
updated 11.5 years ago by
delhomme@embl.de
★ 1.2k • written 11.5 years ago by
Guest User
★ 13k
0
votes
1
reply
1.3k
views
easyRNAseq remove overlapping features
Annotation
BSgenome
BSgenome
IRanges
easyRNASeq
Annotation
BSgenome
BSgenome
IRanges
updated 11.3 years ago by
delhomme@embl.de
★ 1.2k • written 11.3 years ago by
Vince Schulz
▴ 150
0
votes
1
reply
1.4k
views
some problems of easyRNASeq� : about the gtf files
Annotation
easyRNASeq
Annotation
easyRNASeq
updated 11.1 years ago by
delhomme@embl.de
★ 1.2k • written 11.1 years ago by
Guest User
★ 13k
50 results • Page
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Comment: Cannot connect to ExperimentHub server
by
Jiayu
• 0
Many thanks and it also resolved the same issue for me!
Comment: Help with running egsea()
by
Chris
• 0
I tried egsea.ma and got this error: gsa = egsea.ma(numeric_matrix, vector_group, probe_annotation, contrasts = contrast_matrix, gs.an…
Comment: Getting Error in hclust(d, method = method): NA/NaN/Inf in foreign function call
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• 0
Thank you for your response. To clarify, the process of making a heatmap performs rowscaling so it takes the value - (mean/std). And to res…
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sigPathway is another method that does not account for inter-gene correlation and which gives inflated significance, as we showed in our 20…
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by
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