Showing : easyrnaseq • reset
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
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
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
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
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
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
5
replies
2.3k
views
easyRNAseq annotation file
easyrnaseq annotation
8.6 years ago kylvalda • 0
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
8.8 years ago Michael Dondrup ▴ 10
0
votes
2
replies
1.3k
views
simpleRNASeq error importing BAM files
simpleRNASeq easyRNASeq
updated 8.8 years ago by 65k • written 8.8 years ago by • 0
0
votes
6
replies
1.7k
views
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
2
votes
6
replies
1.9k
views
easyRNAseq says Your annotation is not in sync with your alignments!
easyRNAseq
updated 9.2 years ago by ▴ 320 • written 9.2 years ago by • 0
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
1
vote
5
replies
2.1k
views
Getting a count matrix from a SummerizedExpriment with EasyRNASeq
easyrnaseq
9.5 years ago Sylvain Foisy ▴ 80
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
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 ▴ 80 • written 10.1 years ago by ▴ 320
0
votes
1
reply
1.3k
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 41k • written 10.4 years ago by ★ 13k
0
votes
0
replies
1.2k
views
easyRNASeq packages: overlapping exons warning unsolved (?) and use of paired end information
Coverage Annotation GO Cancer Organism edgeR DESeq GenomicRanges easyRNASeq Coverage GO
10.4 years ago 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 ▴ 320 • written 10.4 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 10.4 years ago by ▴ 80 • written 10.4 years ago by ▴ 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 ★ 1.2k • written 10.5 years ago by ★ 13k
0
votes
1
reply
1.3k
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
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
0
replies
1.2k
views
error in "count" for SummarizedExperiment in easyRNASeq
easyRNASeq DESeq2 easyRNASeq DESeq2
10.6 years ago Lescai, Francesco ▴ 380
0
votes
0
replies
1.1k
views
easyRNASeq packages: overlapping exons warning unsolved (?) and use of paired end information
Annotation Organism edgeR DESeq easyRNASeq Annotation Organism edgeR DESeq easyRNASeq
10.9 years ago Gabriele Zoppoli ▴ 50
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 11.0 years ago by ▴ 30 • written 11.1 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
votes
0
replies
1.3k
views
RPKM calculation genewise
Normalization Visualization easyRNASeq Normalization Visualization easyRNASeq
11.1 years ago delhomme@embl.de ★ 1.2k
0
votes
0
replies
841
views
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
replies
959
views
easyRNA adapting annotations to avoid overlapping synthetic exons
Annotation Organism easyRNASeq Annotation Organism easyRNASeq
11.2 years ago Bayles, Darrell ▴ 10
0
votes
0
replies
873
views
easyRNASeq read counts varying when recounting same sample!
Annotation GO biomaRt easyRNASeq Annotation GO biomaRt easyRNASeq
11.2 years ago delhomme@embl.de ★ 1.2k
0
votes
0
replies
792
views
easyRNASeq read counts varying when recounting same sample!
biomaRt easyRNASeq biomaRt easyRNASeq
11.2 years ago René ▴ 30
0
votes
1
reply
1.4k
views
Problems in running easyRNASeq
Annotation Organism DEGseq easyRNASeq Annotation Organism DEGseq easyRNASeq
updated 11.2 years ago by ★ 1.2k • written 11.2 years ago by ★ 13k
0
votes
2
replies
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
1.3k
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
0
replies
1.6k
views
Error message with transcriptCounts(easyRNASeq) performed with gtf file generated with cuffmerge
RNASeq Annotation Normalization Cancer Organism BSgenome BSgenome easyRNASeq RNASeq
11.3 years ago Richard Friedman ★ 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 11.4 years ago by ★ 1.2k • written 11.4 years ago by ★ 2.0k
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
1
reply
993
views
easyRNASeq and edgeR
BSgenome BSgenome edgeR easyRNASeq BSgenome BSgenome edgeR easyRNASeq
updated 11.4 years ago by ★ 1.2k • written 11.4 years ago by ★ 13k
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
votes
0
replies
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
0
replies
747
views
bam files in sub-directories
easyRNASeq easyRNASeq
11.5 years ago RenéBöttcher ▴ 20
0
votes
1
reply
848
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
0
replies
849
views
question on easyRNASeq developer version
GLAD easyRNASeq GLAD easyRNASeq
11.5 years ago delhomme@embl.de ★ 1.2k
0
votes
0
replies
904
views
get synthetic exon dataset with easyRNASeq
RNASeq Annotation Normalization GO PROcess easyRNASeq RNASeq Annotation Normalization GO
11.5 years ago delhomme@embl.de ★ 1.2k
0
votes
1
reply
851
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
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
50 results • Page 1 of 1
Recent ...
Replies
Comment: Reproducibility issue with scran together with lapply and BiocParallel by ATpoint ★ 4.0k
Thanks Aaron for the response. RNGseed (for me) has no effect. I actually stumbled over this in one of my analysis where I have a constant …
Comment: Opposite sign of LFC in count plots of DEGs (DESeq2) by winwater0928 • 0
Thank you for your comment! 1)"Your contrast is comparing LGR5 to Homeostasis." means (Lgr5)/(Homeostasis). Is it right? Then, I think if…
Answer: Reproducibility issue with scran together with lapply and BiocParallel by Aaron Lun ★ 28k
IIRC **BiocParallel** switches to a different RNG when inside its own functions like `bplapply` - specifically L'Ecuyer-CMRG, as opposed to…
Comment: DESeq2 output used for PCA plot on R studio by swbarnes2 ★ 1.3k
This looks terrible for RNASeq data, because it's not RNASeq data. It's a matrix of pretty random numbers, which you know because you poste…
Comment: DESeq2 output used for PCA plot on R studio by Aaliya • 0
I had taken this code from internet, but after reading about it and I did on my own, I would be making a post to ask for the suggestions if…
Votes
C: null model and DEXSeqDataSet object in DEXSEQ
A: Are published RNA seq data analyses often wrong in calculating p-values and FDR?
A: How to explain how DESeq2 works to someone with zero bioinformatics background?
Answer: Interpret plot from DiffBind
Answer: How to retrieve gene ontology GO class from gene list?
Awards • All
Supporter to JKim • 0
Popular Question to Gordon Smyth 50k
Popular Question to Chris • 0
Supporter to Jonathan ▴ 10
Popular Question to Bine ▴ 40
Locations • All
Germany, 2 minutes ago
France, 5 minutes ago
Finland, 5 minutes ago
France, 7 minutes ago
Portugal, 11 minutes ago
Traffic: 934 users visited in the last hour
Content Search
Users
Tags
Badges
Help About
FAQ
Access RSS
API
Stats

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.

Powered by the version 2.3.6