Showing : easyrnaseq • reset
0
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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
1
vote
13
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3.0k
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Several issues with the package easyRNASeq
easyrnaseq bug
8.9 years ago • updated 8.8 years ago Michael Dondrup ▴ 10
0
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5
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2.3k
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easyRNAseq annotation file
easyrnaseq annotation
8.7 years ago kylvalda • 0
2
votes
6
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2.0k
views
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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4
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1.7k
views
easyRNASeq error
Sequencing Alignment Annotation Organism BSgenome biomaRt BSgenome easyRNASeq Sequencing
12.2 years ago delhomme@embl.de ★ 1.2k
0
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2
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1.3k
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easyRNASeq install problem
easyRNASeq easyRNASeq
updated 11.8 years ago by 21k • written 11.8 years ago by ▴ 50
0
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3
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1.9k
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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
votes
7
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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 ★ 1.2k • written 11.4 years ago by ★ 2.0k
1
vote
5
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2.1k
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Getting a count matrix from a SummerizedExpriment with EasyRNASeq
easyrnaseq
9.5 years ago Sylvain Foisy ▴ 80
0
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2
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2.5k
views
counting RNA-seq reads in R/BioC
GO Infrastructure Rsubread easyRNASeq GO Infrastructure Rsubread easyRNASeq
updated 11.7 years ago by ★ 6.8k • written 11.7 years ago by ▴ 880
0
votes
6
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1.3k
views
question on easyRNASeq developer version
easyRNASeq easyRNASeq
updated 11.6 years ago by ▴ 20 • written 11.6 years ago by ★ 1.2k
0
votes
8
replies
2.0k
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Using easyRNASeq package: question about BAM/BAI and links to them
easyRNASeq easyRNASeq
updated 10.5 years ago by ▴ 80 • written 10.5 years ago by ▴ 80
4
votes
5
replies
1.4k
views
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
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 10.5 years ago by ▴ 10
0
votes
2
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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
0
votes
2
replies
1.0k
views
easyRNAseq question
Category DESeq easyRNASeq Category DESeq easyRNASeq
updated 11.8 years ago by ★ 13k • written 11.9 years ago by ▴ 190
0
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6
replies
1.7k
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easyRNASeq: "Error in IRangesList"
easyRNASeq
8.9 years ago surjray • 0
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 ▴ 320 • written 9.2 years ago by ▴ 80
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 ★ 1.2k • written 11.7 years ago by ★ 13k
0
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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 ▴ 320 • written 10.4 years ago by 50k
0
votes
1
reply
1.9k
views
Using a countDataSet as input data in DESeq2
easyRNASeq easyRNASeq
updated 10.4 years ago by 42k • written 10.4 years ago by ★ 13k
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
811
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
4
replies
1.1k
views
easyRNAseq question
easyRNASeq easyRNASeq
updated 12.0 years ago by ▴ 190 • written 12.0 years ago by ★ 1.2k
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
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
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2
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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
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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
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
858
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
1.4k
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
2
replies
1.3k
views
error message with easyRNASeq use case
RNASeq Cancer Organism easyRNASeq RNASeq Cancer Organism easyRNASeq
updated 11.5 years ago by 65k • written 11.5 years ago by ★ 2.0k
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
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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
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
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
0
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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 ▴ 30 • written 11.1 years ago by ★ 13k
0
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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
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 ★ 1.2k • written 10.7 years ago by ★ 13k
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 ★ 1.2k • written 10.6 years ago by ▴ 10
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 ★ 1.2k • written 10.5 years ago by ★ 13k
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
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
2
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1.3k
views
simpleRNASeq error importing BAM files
simpleRNASeq easyRNASeq
updated 8.9 years ago by 65k • written 8.9 years ago by • 0
0
votes
17
replies
2.8k
views
Issue with easyRNASeq
easyRNASeq error
8.8 years ago 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 25k • written 8.6 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
3
replies
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
0
replies
888
views
reads of different lengths (easyRNASeq)
Annotation Organism BSgenome convert BSgenome easyRNASeq Annotation Organism BSgenome
11.9 years ago delhomme@embl.de ★ 1.2k
50 results • Page 1 of 1
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Comment: How to use bootRanges to bootstrap small RNA loci (nullranges package) by Michael Love 42k
I'll take a look later. For next time, I've edited your post by enclosing the code in triple backticks (on their own link). This properly …
Comment: deseq2 results by sajadahmad41454 • 0
could you please tell me if the results are fine or not? ![pca summary][1] ![pca plot][2] [1]: /media/images/ee7d8693-bcbe-4a7a-a566-d3…
Answer: normalization using Deseq2 by ATpoint ★ 4.1k
counts(dds, normalized=TRUE)
Comment: How to use bootRanges to bootstrap small RNA loci (nullranges package) by Poonam • 0
Hi Michael, I have tried what you suggested. I started with methylation loci. I created segment1 and segment2 but how to combine them bec…
Comment: EGSEA usage with microarray data (with vooma)? by Chris • 0
Hi Pekka, I also try EGSEA with microarray data. However, I got this error. Would you please have a suggestion? gsa = egsea.ma(numeric…
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A: Volcanoplot with limma - RAW P-values or Adj.P-Values
Answer: Mac ARM64 build report for BioC 3.19 from 'kjohnson3' reporting ERROR which it
Comment: Mac ARM64 build report for BioC 3.19 from 'kjohnson3' reporting ERROR which it
Answer: minfi latest update for EPIC V2 chip
A: Error in DESeqDataSet : some values in assay are not integers
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