Showing : easyrnaseq • reset
1
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2
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2.8k
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mgcv not updating
mgcv easyRNASeq
updated 3.8 years ago by 25k • written 3.8 years ago by ▴ 10
0
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3
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1.4k
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simpleRNASeq easyRNAseq warnings edgeR error
simplernaseq easyrnaseq edger DEformats
updated 6.8 years ago by ▴ 320 • written 7.0 years ago by • 0
4
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5
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1.7k
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Warning: missing reverse strand option in easyRNASeq.
easyrnaseq rnaseq strand
updated 7.5 years ago by 16k • written 7.5 years ago by ▴ 10
0
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1
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1.6k
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simpleRNASeq stopped running (related to S4 vectors?)
simplernaseq easyrnaseq s4vectors
updated 9.0 years ago by ▴ 320 • written 9.0 years ago by • 0
0
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2
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1.8k
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Package installation errors for Bioconductor and easyRNASeq
installation biocinstaller easyrnaseq
updated 9.0 years ago by 25k • written 9.0 years ago by • 0
2
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2
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1.6k
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Error reading BAM file with duplicated header in easyRNAseq and GenomicAlignments
software error easyrnaseq genomicalignments bam
updated 9.2 years ago by 25k • written 9.2 years ago by ▴ 10
0
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5
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2.5k
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easyRNAseq annotation file
easyrnaseq annotation
9.3 years ago kylvalda • 0
0
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17
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3.2k
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Issue with easyRNASeq
easyRNASeq error
9.5 years ago ea11g0 • 0
1
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13
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3.4k
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Several issues with the package easyRNASeq
easyrnaseq bug
9.5 years ago Michael Dondrup ▴ 10
0
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2
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1.4k
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simpleRNASeq error importing BAM files
simpleRNASeq easyRNASeq
updated 9.5 years ago by 67k • written 9.5 years ago by • 0
0
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6
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1.9k
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easyRNASeq: "Error in IRangesList"
easyRNASeq
9.5 years ago surjray • 0
0
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5
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2.8k
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count tables created with easyRNASeq and the rpkm() function from edgeR
easyrnaseq edger rpkm
updated 9.8 years ago by ▴ 320 • written 9.9 years ago by ▴ 80
2
votes
6
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2.2k
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easyRNAseq says Your annotation is not in sync with your alignments!
easyRNAseq
updated 9.9 years ago by ▴ 320 • written 9.9 years ago by • 0
0
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1
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3.4k
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easyRNASeq error: Error in aggregate.data.frame(as.data.frame(x), ...) : no rows to aggregate
easyrnaseq
10.1 years ago sylvian • 0
1
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5
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2.3k
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Getting a count matrix from a SummerizedExpriment with EasyRNASeq
easyrnaseq
10.2 years ago Sylvain Foisy ▴ 80
0
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1
reply
1.3k
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Devel version of easyRNASeq: using the simpleRNASeq method gives an error
easyRNASeq easyRNASeq
updated 10.7 years ago by ▴ 320 • written 10.7 years ago by ▴ 80
0
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2
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1.5k
views
Devel version of easyRNASeq: using the simpleRNASeq method gives an error
Annotation easyRNASeq Annotation easyRNASeq
updated 10.7 years ago by ▴ 80 • written 10.7 years ago by ▴ 320
0
votes
1
reply
1.6k
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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 11.1 years ago by ▴ 320 • written 11.1 years ago by 52k
0
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1
reply
2.1k
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Using a countDataSet as input data in DESeq2
easyRNASeq easyRNASeq
updated 11.1 years ago by 43k • written 11.1 years ago by ★ 13k
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0
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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 easyRNASeq Coverage GO
11.1 years ago Nicolas Delhomme ▴ 320
0
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2
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1.7k
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easyRNAseq and DEseq for no replicate RNAseq
RNASeq PROcess easyRNASeq RNASeq PROcess easyRNASeq
updated 11.1 years ago by ▴ 320 • written 11.1 years ago by ▴ 10
0
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8
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2.3k
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Using easyRNASeq package: question about BAM/BAI and links to them
easyRNASeq easyRNASeq
updated 11.1 years ago by ▴ 80 • written 11.1 years ago by ▴ 80
0
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7
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3.0k
views
GTF file error when using easyRNAseq�
Annotation Organism BSgenome BSgenome DESeq easyRNASeq Annotation Organism BSgenome DESeq
updated 11.1 years ago by ★ 1.2k • written 11.1 years ago by ★ 13k
0
votes
1
reply
1.5k
views
eayRNASeq with Ensemble GRCh37 help
Annotation Organism easyRNASeq DESeq2 Annotation Organism easyRNASeq DESeq2
updated 11.3 years ago by ★ 1.2k • written 11.3 years ago by ▴ 10
0
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5
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1.9k
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EasyRNAseq - error in building count table - Error in unlist
Sequencing RNASeq edgeR easyRNASeq Sequencing RNASeq edgeR easyRNASeq
updated 11.3 years ago by ★ 1.2k • written 11.3 years ago by ★ 13k
0
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0
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1.3k
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error in "count" for SummarizedExperiment in easyRNASeq
easyRNASeq DESeq2 easyRNASeq DESeq2
11.3 years ago Lescai, Francesco ▴ 380
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
Annotation Organism edgeR DESeq easyRNASeq Annotation Organism edgeR DESeq easyRNASeq
11.6 years ago Gabriele Zoppoli ▴ 50
0
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1
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1.2k
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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 11.7 years ago by ▴ 30 • written 11.7 years ago by ★ 13k
0
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1
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1.6k
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some problems of easyRNASeq� : about the gtf files
Annotation easyRNASeq Annotation easyRNASeq
updated 11.8 years ago by ★ 1.2k • written 11.8 years ago by ★ 13k
0
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0
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1.5k
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RPKM calculation genewise
Normalization Visualization easyRNASeq Normalization Visualization easyRNASeq
11.8 years ago delhomme@embl.de ★ 1.2k
0
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0
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946
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easyRNA adapting annotations to avoid overlapping synthetic exons
Annotation Organism easyRNASeq Annotation Organism easyRNASeq
11.8 years ago delhomme@embl.de ★ 1.2k
0
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0
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1.1k
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easyRNA adapting annotations to avoid overlapping synthetic exons
Annotation Organism easyRNASeq Annotation Organism easyRNASeq
11.8 years ago Bayles, Darrell ▴ 10
0
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0
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984
views
easyRNASeq read counts varying when recounting same sample!
Annotation GO biomaRt easyRNASeq Annotation GO biomaRt easyRNASeq
11.9 years ago delhomme@embl.de ★ 1.2k
0
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0
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909
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easyRNASeq read counts varying when recounting same sample!
biomaRt easyRNASeq biomaRt easyRNASeq
11.9 years ago René ▴ 30
0
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1
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1.6k
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Problems in running easyRNASeq
Annotation Organism DEGseq easyRNASeq Annotation Organism DEGseq easyRNASeq
updated 11.9 years ago by ★ 1.2k • written 11.9 years ago by ★ 13k
0
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2
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2.4k
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using easyRNASeq to calculate RPKM values
easyRNASeq easyRNASeq
updated 11.9 years ago by ★ 1.2k • written 11.9 years ago by ▴ 260
0
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1
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1.4k
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easyRNAseq remove overlapping features
Annotation BSgenome BSgenome IRanges easyRNASeq Annotation BSgenome BSgenome IRanges
updated 12.0 years ago by ★ 1.2k • written 12.0 years ago by ▴ 160
0
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0
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1.7k
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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
12.0 years ago Richard Friedman ★ 2.0k
0
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7
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2.5k
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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 12.1 years ago by ★ 1.2k • written 12.1 years ago by ★ 2.0k
0
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2
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1.4k
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error message with easyRNASeq use case
RNASeq Cancer Organism easyRNASeq RNASeq Cancer Organism easyRNASeq
updated 12.1 years ago by 67k • written 12.1 years ago by ★ 2.0k
0
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1
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1.1k
views
easyRNASeq and edgeR
BSgenome BSgenome edgeR easyRNASeq BSgenome BSgenome edgeR easyRNASeq
updated 12.1 years ago by ★ 1.2k • written 12.1 years ago by ★ 13k
0
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3
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2.1k
views
Error: 'devel' version requires a more recent R
GUI Cancer easyRNASeq GUI Cancer easyRNASeq
updated 12.1 years ago by 21k • written 12.1 years ago by ★ 2.0k
0
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0
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1.4k
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get synthetic exon dataset with easyRNASeq
RNASeq Alignment Annotation Normalization GO PROcess GenomicRanges DEXSeq easyRNASeq GO
12.1 years ago delhomme@embl.de ★ 1.2k
0
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1
reply
1.5k
views
error in easyRNASeq
RNASeq BSgenome BSgenome easyRNASeq RNASeq BSgenome BSgenome easyRNASeq
updated 12.1 years ago by ★ 1.2k • written 12.1 years ago by ▴ 510
0
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0
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864
views
bam files in sub-directories
easyRNASeq easyRNASeq
12.1 years ago RenéBöttcher ▴ 20
0
votes
1
reply
966
views
bam files in sub-directories
easyRNASeq easyRNASeq
updated 12.1 years ago by ★ 1.2k • written 12.2 years ago by ★ 13k
0
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0
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971
views
question on easyRNASeq developer version
GLAD easyRNASeq GLAD easyRNASeq
12.2 years ago delhomme@embl.de ★ 1.2k
0
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0
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1.0k
views
get synthetic exon dataset with easyRNASeq
RNASeq Annotation Normalization GO PROcess easyRNASeq RNASeq Annotation Normalization GO
12.2 years ago delhomme@embl.de ★ 1.2k
0
votes
1
reply
976
views
warnings on easyRNASeq package
Annotation Organism PROcess GenomicRanges easyRNASeq Annotation Organism PROcess
updated 12.2 years ago by ▴ 10 • written 12.2 years ago by ★ 1.2k
0
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2
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1.2k
views
RNAseq object
RNASeq DESeq easyRNASeq RNASeq DESeq easyRNASeq
updated 12.2 years ago by ★ 4.2k • written 12.2 years ago by ★ 13k
50 results • Page 1 of 1
Recent ...
Replies
Comment: Cross-validation with multiple control subgroups in limma by Ali Barry ▴ 40
Thanks so much for taking the time here, the insights are much appreciated. I suspected I'd have to ad hoc compare results if I did repeat …
Answer: Cross-validation with multiple control subgroups in limma by Gordon Smyth 52k
limma doesn't do cross-validation or resampling. Like most classical linear modeling procedures in statistics, limma uses a statistical mod…
Comment: Issues with seqlevelsStyle when making custom txdb objects for genomes/annotatio by Robert Castelo ★ 3.4k
Hi Hervé, thank you very much for your input into how to properly build and manage TxDb objects. gDNAx has two main inputs, one or more BAM…
Comment: Biostrings: Error writing long reads (>200 kbps) with writeQualityScaledXStringS by Aidan ▴ 60
Quick update: this is fixed in a branch awaiting PR to Biostrings (https://github.com/Bioconductor/Biostrings/pull/122). Should be in `deve…
Answer: Can DESeq2's design compensate for sequencing experimental design shortcomings? by Michael Love 43k
For statistical analysis plans, I recommend working with a local statistician or someone familiar with linear models in R. I have to reserv…
Votes
C: edgeR and lack of counts ID on CPM matrix
A: DESeq2 Following RSEM
A: importing RSEM data into DESeq2
A: Expected counts from RSEM in DESeq2
A: Using RSEM reads for DESeq2
Awards • All
Popular Question to Ali Barry ▴ 40
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Popular Question to Jenny Drnevich ★ 2.0k
Popular Question to martin.grigorov ▴ 10
Scholar to James W. MacDonald 67k
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