Showing : easyRNAseq • reset
4
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5
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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
2
votes
2
replies
1.4k
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Error reading BAM file with duplicated header in easyRNAseq and GenomicAlignments
software error easyrnaseq genomicalignments bam
updated 8.6 years ago by 25k • written 8.7 years ago by ▴ 10
2
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6
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2.0k
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easyRNAseq says Your annotation is not in sync with your alignments!
easyRNAseq
updated 9.3 years ago by ▴ 320 • written 9.3 years ago by • 0
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 Michael Dondrup ▴ 10
1
vote
5
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2.1k
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Getting a count matrix from a SummerizedExpriment with EasyRNASeq
easyrnaseq
9.6 years ago Sylvain Foisy ▴ 80
1
vote
2
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2.4k
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mgcv not updating
mgcv easyRNASeq
updated 3.2 years ago by 25k • written 3.2 years ago by ▴ 10
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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1
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1.0k
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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
817
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
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1.1k
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easyRNAseq question
easyRNASeq easyRNASeq
updated 12.0 years ago by ▴ 190 • written 12.0 years ago by ★ 1.2k
0
votes
2
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1.0k
views
easyRNAseq question
Category DESeq easyRNASeq Category DESeq easyRNASeq
updated 11.9 years ago by ★ 13k • written 11.9 years ago by ▴ 190
0
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0
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890
views
reads of different lengths (easyRNASeq)
Annotation Organism BSgenome convert BSgenome easyRNASeq Annotation Organism BSgenome
11.9 years ago delhomme@embl.de ★ 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
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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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1
reply
897
views
Regarding an issue with easyRNASeq - from Surjyendu Ray.
Organism edgeR easyRNASeq Organism edgeR easyRNASeq
11.8 years ago • updated 11.7 years ago delhomme@embl.de ★ 1.2k
0
votes
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
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 11.7 years ago by ★ 1.2k • written 11.7 years ago by ★ 13k
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 11.7 years ago by ★ 1.2k
0
votes
2
replies
1.3k
views
Error of GTF Annotation in easyRNASeq
miRNA Annotation easyRNASeq miRNA Annotation easyRNASeq
11.7 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
862
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
0
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916
views
get synthetic exon dataset with easyRNASeq
RNASeq Annotation Normalization GO PROcess easyRNASeq RNASeq Annotation Normalization GO
11.6 years ago delhomme@embl.de ★ 1.2k
0
votes
0
replies
864
views
question on easyRNASeq developer version
GLAD easyRNASeq GLAD easyRNASeq
11.6 years ago delhomme@embl.de ★ 1.2k
0
votes
1
reply
861
views
bam files in sub-directories
easyRNASeq easyRNASeq
updated 11.6 years ago by ★ 1.2k • written 11.6 years ago by ★ 13k
0
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0
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763
views
bam files in sub-directories
easyRNASeq easyRNASeq
11.6 years ago RenéBöttcher ▴ 20
0
votes
0
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1.3k
views
get synthetic exon dataset with easyRNASeq
RNASeq Alignment Annotation Normalization GO PROcess GenomicRanges DEXSeq easyRNASeq GO
11.5 years ago 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 ★ 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
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2
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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
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 11.5 years ago by ★ 1.2k • written 11.5 years ago by ★ 2.0k
0
votes
0
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1.6k
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Error message with transcriptCounts(easyRNASeq) performed with gtf file generated with cuffmerge
RNASeq Annotation Normalization Cancer Organism BSgenome BSgenome easyRNASeq RNASeq
11.4 years ago Richard Friedman ★ 2.0k
0
votes
1
reply
1.3k
views
easyRNAseq remove overlapping features
Annotation BSgenome BSgenome IRanges easyRNASeq Annotation BSgenome BSgenome IRanges
updated 11.4 years ago by ★ 1.2k • written 11.4 years ago by ▴ 150
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
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
0
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886
views
easyRNASeq read counts varying when recounting same sample!
Annotation GO biomaRt easyRNASeq Annotation GO biomaRt easyRNASeq
11.3 years ago delhomme@embl.de ★ 1.2k
0
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0
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802
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easyRNASeq read counts varying when recounting same sample!
biomaRt easyRNASeq biomaRt easyRNASeq
11.3 years ago René ▴ 30
0
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0
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974
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easyRNA adapting annotations to avoid overlapping synthetic exons
Annotation Organism easyRNASeq Annotation Organism easyRNASeq
11.2 years ago Bayles, Darrell ▴ 10
0
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0
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853
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easyRNA adapting annotations to avoid overlapping synthetic exons
Annotation Organism easyRNASeq Annotation Organism easyRNASeq
11.2 years ago delhomme@embl.de ★ 1.2k
0
votes
0
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1.3k
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RPKM calculation genewise
Normalization Visualization easyRNASeq Normalization Visualization easyRNASeq
11.2 years ago delhomme@embl.de ★ 1.2k
0
votes
1
reply
1.4k
views
some problems of easyRNASeq� : about the gtf files
Annotation easyRNASeq Annotation easyRNASeq
updated 11.2 years ago by ★ 1.2k • written 11.2 years ago by ★ 13k
0
votes
5
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2.4k
views
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
votes
0
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1.1k
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easyRNASeq packages: overlapping exons warning unsolved (?) and use of paired end information
Annotation Organism edgeR DESeq easyRNASeq Annotation Organism edgeR DESeq easyRNASeq
11.0 years ago Gabriele Zoppoli ▴ 50
0
votes
2
replies
1.3k
views
Devel version of easyRNASeq: using the simpleRNASeq method gives an error
Annotation easyRNASeq Annotation easyRNASeq
updated 10.2 years ago by ▴ 80 • written 10.2 years ago by ▴ 320
0
votes
5
replies
1.7k
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 10.7 years ago by ★ 1.2k • written 10.7 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
2
replies
1.5k
views
easyRNAseq and DEseq for no replicate RNAseq
RNASeq PROcess easyRNASeq RNASeq PROcess easyRNASeq
updated 10.5 years ago by ▴ 320 • written 10.5 years ago by ▴ 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 ▴ 80 • written 10.5 years ago by ▴ 80
0
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0
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1.2k
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easyRNASeq packages: overlapping exons warning unsolved (?) and use of paired end information
Coverage Annotation GO Cancer Organism edgeR DESeq GenomicRanges easyRNASeq Coverage GO
10.5 years ago Nicolas Delhomme ▴ 320
0
votes
1
reply
1.2k
views
Devel version of easyRNASeq: using the simpleRNASeq method gives an error
easyRNASeq easyRNASeq
updated 10.2 years ago by ▴ 320 • written 10.2 years ago by ▴ 80
50 results • Page 1 of 1
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Answer: Numerical differences in DESeq2 output depending on different design matrix cons by Michael Love 42k
Yes there can be small numerical differences in the estimated quantities because of how the algorithms decide to stop iterating.
Answer: DESeq2- Mysterious interaction suppresses DEGs by Michael Love 42k
Removing samples from one group nevertheless changes the variance estimation (dispersion) for all comparisons. So you could have pushed one…
Comment: Numerical differences in DESeq2 output depending on different design matrix cons by JKim • 0
The 1st model has an interaction term, but the 2nd model doesn't have the interaction term. That makes the difference.
Comment: Ensembl plants at annotationHub? by Daniele • 0
Hi, I'm using Ensembl Plants release 59 with the IWGSC RefSeq v1.1 gene annotation. Thanks a lot for replying so quickly!
Comment: Numerical differences in DESeq2 output depending on different design matrix cons by swbarnes2 ★ 1.4k
If you restrict yourself to, say, genes with a baseMean > 50, are the numerical differences between the two designs significant?
Votes
Answer: Error while installing BiocManager::install("org.Vdahliae.eg.db")
Comment: How can I create a eigencorplot of pca created from deseq2 object with PCAtools
Answer: Importing a GraphNEL into Cytoscape with RCy3 with error: "Error in cyrestPUT(pa
Answer: Importing a GraphNEL into Cytoscape with RCy3 with error: "Error in cyrestPUT(pa
Rsubread counting peaks ATACseq
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