Showing : easyRNAseq • reset
1
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mgcv not updating
mgcv easyRNASeq
updated 3.3 years ago by 25k • written 3.3 years ago by ▴ 10
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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 6.3 years ago by ▴ 320 • written 6.4 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 7.0 years ago by 16k • written 7.0 years ago by ▴ 10
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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 8.5 years ago by ▴ 320 • written 8.5 years ago by • 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 8.5 years ago by 25k • written 8.5 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 8.7 years ago by 25k • written 8.7 years ago by ▴ 10
0
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5
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2.4k
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easyRNAseq annotation file
easyrnaseq annotation
8.8 years ago kylvalda • 0
0
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17
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2.9k
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Issue with easyRNASeq
easyRNASeq error
9.0 years ago • updated 8.9 years ago ea11g0 • 0
1
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13
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3.1k
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Several issues with the package easyRNASeq
easyrnaseq bug
9.0 years ago • updated 8.9 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 9.0 years ago by 66k • written 9.0 years ago by • 0
0
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6
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1.8k
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easyRNASeq: "Error in IRangesList"
easyRNASeq
9.0 years ago surjray • 0
0
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5
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2.6k
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count tables created with easyRNASeq and the rpkm() function from edgeR
easyrnaseq edger rpkm
updated 9.3 years ago by ▴ 320 • written 9.3 years ago by ▴ 80
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 9.4 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
9.6 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
9.6 years ago Sylvain Foisy ▴ 80
0
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1
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1.2k
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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
0
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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 10.2 years ago by ▴ 80 • written 10.2 years ago by ▴ 320
0
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1
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1.4k
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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 10.5 years ago by ▴ 320 • written 10.5 years ago by 51k
0
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1
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1.9k
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Using a countDataSet as input data in DESeq2
easyRNASeq easyRNASeq
updated 10.5 years ago by 42k • written 10.5 years ago by ★ 13k
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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
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2
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1.6k
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easyRNAseq and DEseq for no replicate RNAseq
RNASeq PROcess easyRNASeq RNASeq PROcess easyRNASeq
updated 10.6 years ago by ▴ 320 • written 10.6 years ago by ▴ 10
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 10.6 years ago by ▴ 80 • written 10.6 years ago by ▴ 80
0
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7
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2.7k
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GTF file error when using easyRNAseq�
Annotation Organism BSgenome BSgenome DESeq easyRNASeq Annotation Organism BSgenome DESeq
updated 10.6 years ago by ★ 1.2k • written 10.6 years ago by ★ 13k
0
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1
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1.4k
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eayRNASeq with Ensemble GRCh37 help
Annotation Organism easyRNASeq DESeq2 Annotation Organism easyRNASeq DESeq2
updated 10.8 years ago by ★ 1.2k • written 10.8 years ago by ▴ 10
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5
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1.7k
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EasyRNAseq - error in building count table - Error in unlist
Sequencing RNASeq edgeR easyRNASeq Sequencing RNASeq edgeR easyRNASeq
updated 10.8 years ago by ★ 1.2k • written 10.8 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
10.8 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
11.0 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 11.2 years ago by ▴ 30 • written 11.2 years ago by ★ 13k
0
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1
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1.5k
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some problems of easyRNASeq� : about the gtf files
Annotation easyRNASeq Annotation easyRNASeq
updated 11.2 years ago by ★ 1.2k • written 11.3 years ago by ★ 13k
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0
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1.4k
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RPKM calculation genewise
Normalization Visualization easyRNASeq Normalization Visualization easyRNASeq
11.3 years ago delhomme@embl.de ★ 1.2k
0
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0
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862
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easyRNA adapting annotations to avoid overlapping synthetic exons
Annotation Organism easyRNASeq Annotation Organism easyRNASeq
11.3 years ago delhomme@embl.de ★ 1.2k
0
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0
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985
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easyRNA adapting annotations to avoid overlapping synthetic exons
Annotation Organism easyRNASeq Annotation Organism easyRNASeq
11.3 years ago Bayles, Darrell ▴ 10
0
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0
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893
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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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812
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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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1
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1.4k
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Problems in running easyRNASeq
Annotation Organism DEGseq easyRNASeq Annotation Organism DEGseq easyRNASeq
updated 11.4 years ago by ★ 1.2k • written 11.4 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 11.4 years ago by ★ 1.2k • written 11.4 years ago by ▴ 260
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1
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1.3k
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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
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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
11.5 years ago Richard Friedman ★ 2.0k
0
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7
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2.3k
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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 11.5 years ago by ★ 1.2k • written 11.5 years ago by ★ 2.0k
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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 11.6 years ago by 66k • written 11.6 years ago by ★ 2.0k
0
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1
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1.0k
views
easyRNASeq and edgeR
BSgenome BSgenome edgeR easyRNASeq BSgenome BSgenome edgeR easyRNASeq
updated 11.6 years ago by ★ 1.2k • written 11.6 years ago by ★ 13k
0
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3
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2.0k
views
Error: 'devel' version requires a more recent R
GUI Cancer easyRNASeq GUI Cancer easyRNASeq
updated 11.6 years ago by 21k • written 11.6 years ago by ★ 2.0k
0
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0
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1.3k
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get synthetic exon dataset with easyRNASeq
RNASeq Alignment Annotation Normalization GO PROcess GenomicRanges DEXSeq easyRNASeq GO
11.6 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 11.6 years ago by ★ 1.2k • written 11.6 years ago by ▴ 510
0
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0
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772
views
bam files in sub-directories
easyRNASeq easyRNASeq
11.6 years ago RenéBöttcher ▴ 20
0
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1
reply
871
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
replies
870
views
question on easyRNASeq developer version
GLAD easyRNASeq GLAD easyRNASeq
11.7 years ago delhomme@embl.de ★ 1.2k
0
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0
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924
views
get synthetic exon dataset with easyRNASeq
RNASeq Annotation Normalization GO PROcess easyRNASeq RNASeq Annotation Normalization GO
11.7 years ago delhomme@embl.de ★ 1.2k
0
votes
1
reply
871
views
warnings on easyRNASeq package
Annotation Organism PROcess GenomicRanges easyRNASeq Annotation Organism PROcess
updated 11.7 years ago by ▴ 10 • written 11.7 years ago by ★ 1.2k
0
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2
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1.1k
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RNAseq object
RNASeq DESeq easyRNASeq RNASeq DESeq easyRNASeq
updated 11.7 years ago by ★ 4.2k • written 11.7 years ago by ★ 13k
50 results • Page 1 of 1
Recent ...
Replies
Comment: gds in GEOmetadb 2023-06-26 version is empty by Frederico Moraes Ferreira ▴ 100
Try axel -n 20 https://gbnci.cancer.gov/geo/GEOmetadb.sqlite.gz
Comment: Most enriched pathway is not expressed when modifying universe parameter by James W. MacDonald 66k
The default for `enrichGO` is to subset to those with a p-value<0.05. You don't adjust that default argument, so you shouldn't have any GO …
Answer: In a 3 group DEG analysis with three batches, can I use 1 group in all three bat by Michael Love 42k
You can compare A and C thanks to the sharing of samples from B across 1, 2 and 3.
Comment: Most enriched pathway is not expressed when modifying universe parameter by adripel • 0
In the enrichGO results we have significant and non-significant enriched terms that are displayed. So why would an enriched term (significa…
Answer: Design formula, numeric contrast, and lfcshrink in deseq2 by Michael Love 42k
For questions about how to construct the correct contrasts correspond to particular hypotheses, I recommend consulting with a local statist…
Votes
Comment: Most enriched pathway is not expressed when modifying universe parameter
Time-course, comparison of two groups
Answer: Behaviour of featureCounts when quantifying multi-mapping reads
Answer: GESA with certain gene list returns no result with human genom, but many result
Answer: Odd behavior of Rsubread::featureCounts when setting `nonOverlap = 0`
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Popular Question to richardallenfriedmanbrooklyn ▴ 20
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