Showing : easyRNASeq • reset
1
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2
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2.3k
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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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3
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1.2k
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simpleRNASeq easyRNAseq warnings edgeR error
simplernaseq easyrnaseq edger DEformats
updated 6.2 years ago by ▴ 320 • written 6.3 years ago by • 0
4
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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
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1
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1.4k
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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
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2
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1.6k
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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
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2
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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 8.6 years ago by ▴ 10
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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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17
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2.8k
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Issue with easyRNASeq
easyRNASeq error
8.8 years ago ea11g0 • 0
1
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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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2
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1.3k
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simpleRNASeq error importing BAM files
simpleRNASeq easyRNASeq
updated 8.8 years ago by 65k • written 8.8 years ago by • 0
0
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6
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1.7k
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easyRNASeq: "Error in IRangesList"
easyRNASeq
8.9 years ago surjray • 0
0
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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
2
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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
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1
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3.2k
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easyRNASeq error: Error in aggregate.data.frame(as.data.frame(x), ...) : no rows to aggregate
easyrnaseq
9.4 years ago sylvian • 0
1
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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
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2
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1.3k
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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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1
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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
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1
reply
1.3k
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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
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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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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
10.4 years ago Nicolas Delhomme ▴ 320
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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2
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1.5k
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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
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
1.4k
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
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5
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1.6k
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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
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0
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1.2k
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error in "count" for SummarizedExperiment in easyRNASeq
easyRNASeq DESeq2 easyRNASeq DESeq2
10.6 years ago Lescai, Francesco ▴ 380
0
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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
10.9 years ago Gabriele Zoppoli ▴ 50
0
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1
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1.1k
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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
reply
1.4k
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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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0
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1.3k
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RPKM calculation genewise
Normalization Visualization easyRNASeq Normalization Visualization easyRNASeq
11.1 years ago delhomme@embl.de ★ 1.2k
0
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0
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842
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
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0
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960
views
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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875
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
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0
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794
views
easyRNASeq read counts varying when recounting same sample!
biomaRt easyRNASeq biomaRt easyRNASeq
11.2 years ago René ▴ 30
0
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1
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1.4k
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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
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2
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2.2k
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using easyRNASeq to calculate RPKM values
easyRNASeq easyRNASeq
updated 11.3 years ago by ★ 1.2k • written 11.3 years ago by ▴ 260
0
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1
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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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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
11.3 years ago Richard Friedman ★ 2.0k
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
0
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2
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1.3k
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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
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1
reply
995
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
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3
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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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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
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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
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0
replies
751
views
bam files in sub-directories
easyRNASeq easyRNASeq
11.5 years ago RenéBöttcher ▴ 20
0
votes
1
reply
850
views
bam files in sub-directories
easyRNASeq easyRNASeq
updated 11.5 years ago by ★ 1.2k • written 11.5 years ago by ★ 13k
0
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0
replies
853
views
question on easyRNASeq developer version
GLAD easyRNASeq GLAD easyRNASeq
11.5 years ago delhomme@embl.de ★ 1.2k
0
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0
replies
905
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
852
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
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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
50 results • Page 1 of 1
Recent ...
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Answer: PCA plot suggestions by Michael Love 41k
For help with interpretation and design of analysis, I recommend working with a local statistician. Due to time restrictions, I can only…
Comment: DESeq2 Error in `.rowNamesDF<-`(x, value = value): Invalid 'row.names' length by ussarizona ▴ 10
Hi Michael, Yes, I could figure it out what does the error mean. In my matrix I had the first colum GeneID while in my condition I only h…
Answer: Deseq2. decontXcounts not integers. Useful alternative? by Michael Love 41k
Another option would be to put the per sample estimated contamination in the design. This is for example how RUV etc help remove spurious D…
Answer: ATACseq merge peaks by ATpoint ★ 4.0k
That depends on your analysis. Typically, for differential analysis (and convenience) you would produce a single set of peaks (e.g. by merg…
Comment: Deseq2. decontXcounts not integers. Useful alternative? by camp ▴ 10
Yes, @atpoint is correct. decontX decontaminated counts are not integers due to the way the variation inference algorithm works, but you ca…
Votes
Comment: DESeq2 Error in `.rowNamesDF<-`(x, value = value): Invalid 'row.names' length
Comment: Deseq2. decontXcounts not integers. Useful alternative?
Comment: Opposite sign of LFC in count plots of DEGs (DESeq2)
biomaRt error: database disk image is malformed
Comment: biomaRt : No lock file for BiocFileCache
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