Showing : easyRNASeq • reset
0
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2.8k
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Issue with easyRNASeq
easyRNASeq error
8.8 years ago ea11g0 • 0
1
vote
13
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3.0k
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Several issues with the package easyRNASeq
easyrnaseq bug
8.8 years ago Michael Dondrup ▴ 10
0
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8
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2.0k
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Using easyRNASeq package: question about BAM/BAI and links to them
easyRNASeq easyRNASeq
updated 10.4 years ago by ▴ 80 • written 10.4 years ago by ▴ 80
0
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7
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2.6k
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GTF file error when using easyRNAseq�
Annotation Organism BSgenome BSgenome DESeq easyRNASeq Annotation Organism BSgenome DESeq
updated 10.5 years ago by ★ 1.2k • written 10.5 years ago by ★ 13k
0
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7
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2.2k
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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 ★ 1.2k • written 11.4 years ago by ★ 2.0k
2
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6
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1.9k
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easyRNAseq says Your annotation is not in sync with your alignments!
easyRNAseq
updated 9.2 years ago by ▴ 320 • written 9.3 years ago by • 0
0
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6
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1.3k
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question on easyRNASeq developer version
easyRNASeq easyRNASeq
updated 11.6 years ago by ▴ 20 • written 11.6 years ago by ★ 1.2k
0
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6
replies
1.7k
views
easyRNASeq: "Error in IRangesList"
easyRNASeq
8.9 years ago surjray • 0
0
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5
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2.3k
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easyRNAseq annotation file
easyrnaseq annotation
8.6 years ago kylvalda • 0
0
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5
replies
1.6k
views
EasyRNAseq - error in building count table - Error in unlist
Sequencing RNASeq edgeR easyRNASeq Sequencing RNASeq edgeR easyRNASeq
updated 10.6 years ago by ★ 1.2k • written 10.6 years ago by ★ 13k
0
votes
5
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2.6k
views
count tables created with easyRNASeq and the rpkm() function from edgeR
easyrnaseq edger rpkm
updated 9.2 years ago by ▴ 320 • written 9.2 years ago by ▴ 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
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1.4k
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Warning: missing reverse strand option in easyRNASeq.
easyrnaseq rnaseq strand
updated 6.9 years ago by 16k • written 6.9 years ago by ▴ 10
0
votes
5
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2.4k
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EasyRNASeq issue (missing bai files)
GO PROcess DESeq easyRNASeq GO PROcess DESeq easyRNASeq
updated 11.8 years ago by ▴ 10 • written 11.8 years ago by ★ 1.2k
0
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4
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1.7k
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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 11.9 years ago by ▴ 190 • written 11.9 years ago by ★ 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 21k • written 11.5 years ago by ★ 2.0k
0
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3
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1.2k
views
simpleRNASeq easyRNAseq warnings edgeR error
simplernaseq easyrnaseq edger DEformats
updated 6.2 years ago by ▴ 320 • written 6.3 years ago by • 0
0
votes
2
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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 ★ 1.2k • written 11.6 years ago by ★ 13k
0
votes
2
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1.0k
views
easyRNAseq question
Category DESeq easyRNASeq Category DESeq easyRNASeq
updated 11.8 years ago by ★ 13k • written 11.8 years ago by ▴ 190
0
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2
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1.3k
views
easyRNASeq install problem
easyRNASeq easyRNASeq
updated 11.8 years ago by 21k • written 11.8 years ago by ▴ 50
0
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2
replies
2.5k
views
counting RNA-seq reads in R/BioC
GO Infrastructure Rsubread easyRNASeq GO Infrastructure Rsubread easyRNASeq
updated 11.6 years ago by ★ 6.8k • written 11.6 years ago by ▴ 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 ★ 4.2k • written 11.6 years ago by ★ 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 65k • written 11.4 years ago by ★ 2.0k
0
votes
2
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2.2k
views
using easyRNASeq to calculate RPKM values
easyRNASeq easyRNASeq
updated 11.3 years ago by ★ 1.2k • written 11.3 years ago by ▴ 260
0
votes
2
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1.3k
views
Devel version of easyRNASeq: using the simpleRNASeq method gives an error
Annotation easyRNASeq Annotation easyRNASeq
updated 10.1 years ago by ▴ 80 • written 10.1 years ago by ▴ 320
0
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2
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1.5k
views
easyRNAseq and DEseq for no replicate RNAseq
RNASeq PROcess easyRNASeq RNASeq PROcess easyRNASeq
updated 10.4 years ago by ▴ 320 • written 10.4 years ago by ▴ 10
0
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2
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1.3k
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simpleRNASeq error importing BAM files
simpleRNASeq easyRNASeq
updated 8.9 years ago by 65k • written 8.9 years ago by • 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 25k • written 8.6 years ago by ▴ 10
0
votes
2
replies
1.6k
views
Package installation errors for Bioconductor and easyRNASeq
installation biocinstaller easyrnaseq
updated 8.4 years ago by 25k • written 8.4 years ago by • 0
1
vote
2
replies
2.3k
views
mgcv not updating
mgcv easyRNASeq
updated 3.2 years ago by 25k • written 3.2 years ago by ▴ 10
0
votes
1
reply
1.9k
views
Using a countDataSet as input data in DESeq2
easyRNASeq easyRNASeq
updated 10.4 years ago by 41k • written 10.4 years ago by ★ 13k
0
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1
reply
1.4k
views
Problems in running easyRNASeq
Annotation Organism DEGseq easyRNASeq Annotation Organism DEGseq easyRNASeq
updated 11.3 years ago by ★ 1.2k • written 11.3 years ago by ★ 13k
0
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1
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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 ▴ 30 • written 11.1 years ago by ★ 13k
0
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1
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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 ▴ 320 • written 10.4 years ago by 50k
0
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1
reply
1.4k
views
eayRNASeq with Ensemble GRCh37 help
Annotation Organism easyRNASeq DESeq2 Annotation Organism easyRNASeq DESeq2
updated 10.6 years ago by ★ 1.2k • written 10.6 years ago by ▴ 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 ▴ 10 • written 11.6 years ago by ★ 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 ▴ 320 • written 10.1 years ago by ▴ 80
0
votes
1
reply
891
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
9.4 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 ★ 1.2k • written 11.8 years ago by ★ 2.0k
0
votes
1
reply
807
views
Problems easyRNASeq
Annotation PROcess easyRNASeq Annotation PROcess easyRNASeq
updated 12.1 years ago by ★ 1.2k • written 12.1 years ago by ▴ 10
0
votes
1
reply
1.4k
views
simpleRNASeq stopped running (related to S4 vectors?)
simplernaseq easyrnaseq s4vectors
updated 8.4 years ago by ▴ 320 • written 8.4 years ago by • 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 ▴ 350 • written 12.2 years ago by ★ 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 ★ 1.2k • written 11.5 years ago by ▴ 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 ★ 1.2k • written 11.5 years ago by ★ 13k
0
votes
1
reply
856
views
bam files in sub-directories
easyRNASeq easyRNASeq
updated 11.5 years ago by ★ 1.2k • written 11.5 years ago by ★ 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 ★ 1.2k • written 11.3 years ago by ▴ 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 ★ 1.2k • written 11.1 years ago by ★ 13k
50 results • Page 1 of 1
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Answer: package goseq seems to be not available on the latest version of R by Gordon Smyth 50k
It is true that goseq isn't available for Bioc 3.19. That is because goseq depends on txbmaker, which is itself not yet available for Bioc…
Answer: limma Intercept vs No-intercept models completely changing DMR results? by James W. MacDonald 65k
This part: ``` design_intercept <- model.matrix(~Alt+Sex+Age+PC1, data=targets_Sherpa) colnames(design_intercept) <- c("AltSHP_LA","Al…
Comment: CombineArrays for EPIC and EPIC V2 by Kim • 0
Thank you Tim, this is a great help in getting me started!
Comment: Too many significant genes when integrating gtex and tcga by Michael Love 41k
Yes, this was one of the aspects we highlighted in the 2014 paper, and it's also in the workflow. Check these places first. Also take a st…
Answer: Too many significant genes when integrating gtex and tcga by James W. MacDonald 65k
See `?results`, in particular the lfcThreshold argument.
Votes
Answer: limma Intercept vs No-intercept models completely changing DMR results?
Answer: CombineArrays for EPIC and EPIC V2
Answer: Too many significant genes when integrating gtex and tcga
Comment: Too many significant genes when integrating gtex and tcga
A: Print Differentially Expressed Exons From Dexseq Results
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