Showing : RNAseq • reset
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meta analysis of clc output(differential expression data )
rnaseq metaseq clc output pvalue meta analysis
updated 8.8 years ago by ▴ 10 • written 8.8 years ago by • 0
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1
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1.4k
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meta analysis of p value data by metaseq package
rnaseq meta-analysis p values
8.8 years ago hassangiahi • 0
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0
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1.4k
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Error in qAlign, QuasR, in paired-end RNA Seq
quasr paired-end reads rnaseq
8.8 years ago guillaume.dachy • 0
3
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3
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2.4k
views
getBM function, search for annotation characteristics with entrezgene filters --> result with duplicates
getBM entrez gene identifiers duplicate rnaseq
8.8 years ago Jose Luis Soto Vázquez • 0
3
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4
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4.1k
views
Simultaneously adding two different covariates in the model gives error in DESeq2.
deseq2 dexseq rnaseq differential gene expression differential exon usage
updated 8.8 years ago by 43k • written 8.8 years ago by ▴ 40
0
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0
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993
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OmicCircos for non human genomes
omiccircos rnaseq plants
8.8 years ago Didi ▴ 10
0
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1
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1.5k
views
featureCounts on read 1 of a paired-end experiment
rnaseq
updated 8.8 years ago by ★ 29k • written 8.8 years ago by • 0
4
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1
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5.4k
views
Rsubread featureCounts with strand information
Rsubread bam rnaseq
updated 8.8 years ago by ★ 29k • written 8.8 years ago by ▴ 110
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0
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1.2k
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Error preprocessReads : Error in writeFastq
quasr rnaseq paired-end reads
8.8 years ago guillaume.dachy • 0
0
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2
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1.5k
views
Error when using EnrichmentBrowser's sbea function with RNA-seq data
EnrichmentBrowser rnaseq
8.8 years ago aichen620 • 0
1
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1
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1.4k
views
RNA-seq: EdgeR's togtags table not correlating to htseq-count's CPM values
edger htseqcounts rnaseq
updated 8.8 years ago by ★ 29k • written 8.8 years ago by • 0
2
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3
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4.6k
views
voom on normalised counts
limma voom rnaseq
updated 8.8 years ago by ★ 29k • written 8.8 years ago by ▴ 40
2
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3
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2.3k
views
DESeq2 log-fold change shrunk to -0.4 instead of zero. Why?
deseq2 rnaseq
8.8 years ago lostisle • 0
0
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1
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1.7k
views
JunctionSeq/DEXSeq: Dispersion plot looks strange (but is fine in DESeq2)
deseq2 junctionseq dexseq estimatedispersions rnaseq
updated 8.8 years ago by ★ 13k • written 8.8 years ago by • 0
1
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3
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4.5k
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DESeq2 analysis for RNAseq data at different time points and different conditions
deseq2 timecourse rnaseq
updated 2.5 years ago by • 0 • written 8.8 years ago by ▴ 30
0
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0
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788
views
MLSeq package output
rnaseq
8.8 years ago jonessara770 ▴ 10
4
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4
replies
2.0k
views
How to isolate gene from a single chromosome, RNA Seq experiment, using R package ?
rnaseq r cummerbund
updated 8.8 years ago by 53k • written 8.9 years ago by • 0
4
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5
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8.2k
views
outlier detection of RNAseq samples
deseq2 rnaseq PCA hierarchical clustering outlier
8.9 years ago wd ▴ 30
0
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3
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2.4k
views
Error in ball gown command
rnaseq ballgown differential gene expression
updated 8.9 years ago by ▴ 650 • written 8.9 years ago by ▴ 10
2
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2
replies
1.4k
views
RNA-seq analysis without replicates using tximport and DESeq2
rnaseq deseq2 tximport
updated 8.9 years ago by 43k • written 8.9 years ago by ▴ 70
1
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1
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1.5k
views
Raw read count Vs EdgeR normzlized read count for RUVg normalization
rnaseq ruvseq normalization
updated 8.9 years ago by ▴ 980 • written 8.9 years ago by ▴ 40
0
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2
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1.2k
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can a batch effect be determined in edgeR with only 2 reps?
edger rnaseq batch effect read length
8.9 years ago Spollen, William G. ▴ 30
2
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3
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2.0k
views
Deseq2 time series question,
rnaseq deseq2 timecourse
updated 8.9 years ago by 43k • written 8.9 years ago by • 0
0
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1
reply
2.0k
views
edgeR estimateGLMRobustDisp fails with and error
rnaseq edger
updated 8.9 years ago by ★ 29k • written 8.9 years ago by ▴ 750
0
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1
reply
819
views
DESeq2 Nested Comparison
deseq2 rnaseq
updated 8.9 years ago by 43k • written 8.9 years ago by • 0
2
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3
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2.6k
views
SystemPipeR: alignments with ambiguous pairing were dumped.
R rnaseq tophat summarizeoverlaps systempiper
updated 8.9 years ago by ★ 1.7k • written 8.9 years ago by • 0
5
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2
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2.3k
views
DESeq2 design matrix for timecourse
deseq2 experimental design timecourse rnaseq model
updated 8.9 years ago by 43k • written 8.9 years ago by ▴ 20
0
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6
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1.8k
views
Using tximport to read in data from sailfish experiment
tximport sailfish rnaseq
updated 8.9 years ago by 43k • written 8.9 years ago by ▴ 10
0
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0
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1.4k
views
Figuring out what long decent Phred value unaligned reads are
rnaseq alignment
9.0 years ago Matthew Thornton ▴ 380
1
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2
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1.4k
views
2-Factor Experiment in edgeR, Effect of no reps in one set and two reps in others
rnaseq edger differential expression dispersion
updated 9.0 years ago by ★ 7.9k • written 9.0 years ago by • 0
3
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5
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1.7k
views
i need to have a package for reads alignment to reference genome
rnaseq
updated 9.0 years ago by ▴ 400 • written 9.0 years ago by • 0
6
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4
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1.9k
views
Combining newer/older RNAseq data, batch correcting
rnaseq limma sva batch effect voom
updated 9.0 years ago by ★ 29k • written 9.0 years ago by ▴ 10
0
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2
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2.1k
views
I'm worried that I can't use "ballgown" well
ballgown rnaseq
updated 9.0 years ago by 68k • written 9.0 years ago by • 0
5
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2
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8.5k
views
ComBat to remove batch effects from RNA Seq data
combat rnaseq
updated 9.0 years ago by ▴ 70 • written 9.0 years ago by ▴ 30
2
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2
replies
1.5k
views
rlog transformation for Time-course data
deseq2 rlog transformation timecourse rnaseq
updated 9.0 years ago by 43k • written 9.0 years ago by • 0
27
votes
7
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17k
views
Usability of ERCC spike-ins in standard RNAseq experiments
RNAseq deseq2 ercc
updated 9.0 years ago by ★ 3.8k • written 9.0 years ago by ▴ 30
3
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3
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1.4k
views
EdgeR design and contrasts questions
rnaseq edger design and contrast matrix
9.0 years ago jjh • 0
0
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1
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1.2k
views
Meta-analysis on rna-seq data without replicates
meta-analysis rnaseq metarnaseq
updated 9.0 years ago by 43k • written 9.0 years ago by ▴ 20
1
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10
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2.8k
views
edgeR: AveLogCPM after estimateGLMCommonDisp
rnaseq edger
updated 9.0 years ago by 53k • written 9.0 years ago by ▴ 90
0
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2
replies
1.9k
views
DESeq2 Model matrix design: Merging large RNAseq projects
deseq2 model.matrix batch effect rnaseq
9.0 years ago arom2 • 0
5
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6
replies
7.3k
views
How featureCounts define the gene length
featurecounts rnaseq rsubread
updated 3.8 years ago by 53k • written 9.0 years ago by ▴ 20
0
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3
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2.3k
views
Unable to get soft threshold power using WGCNA for RNA-seq data
rnaseq wgcna picksoftthreshold
updated 9.0 years ago by ▴ 760 • written 9.0 years ago by • 0
0
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1
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2.6k
views
Merging files with gene expression data
merge rnaseq files
updated 9.0 years ago by • 0 • written 9.0 years ago by ▴ 70
3
votes
7
replies
1.9k
views
Weird results (ribosomal proteins / Y-linked genes) in limma/voom
limma voom rnaseq
updated 9.0 years ago by 53k • written 9.0 years ago by ▴ 10
1
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5
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1.5k
views
How to analyze unannotated lncRNA using RNA-seq data?
rnaseq
9.0 years ago xiaoyonf • 0
19
votes
6
replies
47k
views
How to map all Ensembl IDs to Gene Symbols- Problem with AnootationDbi
rnaseq annotationdbi
updated 9.0 years ago by ★ 6.8k • written 9.1 years ago by ▴ 70
1
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2
replies
869
views
rnaseq with DESeq am i doing it right ?
rnaseq deseq2
9.1 years ago • updated 9.0 years ago bioinformatics ▴ 20
2
votes
5
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1.8k
views
Limma-Voom which of two models is correct?
limma-voom rnaseq differential gene expression
9.0 years ago Javier Gutierrez-Achury • 0
0
votes
1
reply
879
views
about sets of replicates in RNA-seq and quality controls
rnaseq limma edgeR deseq2
updated 9.0 years ago by ★ 3.8k • written 9.0 years ago by ▴ 670
2
votes
4
replies
1.1k
views
RNA Seq Analytic Design
rnaseq deseq2
9.0 years ago lauren.fitch • 0
1,409 results • Page 19 of 29
Recent ...
Replies
Comment: Help with defining groups by Phinney, Brett ▴ 10
I got it working , thank you!!!
Comment: Check removeBatchEffect effectiveness by massimo • 0
I would kindly ask for additional support. When not including the design_timepoint argument in removeBatchEffect and thus keeping the inter…
Comment: Error Loading Experiment from SimBenchData Package by ksankaran • 0
Aha, that was it! The object was class Seurat, but I didn't have it installed. After installing, everything works as expected.
Comment: Streamlining the computing time for MiloDE p-value correction in large dataset? by ATpoint ★ 5.0k
Is a method that is so computationally expensive really beneficial and necessary? You seem to have biological replication, don't you, so ps…
Answer: NA values for DESeq2 p-values and adjusted p-values using large sample sizes by ATpoint ★ 5.0k
Outliers without replacement, independent filtering or all-zero counts for that gene. That's the three options that trigger NAs https://bio…
Votes
Comment: Check removeBatchEffect effectiveness
Gene expression associated with continuous (quantitative) traits (Limma/edgeR/correlation)
Answer: Error Loading Experiment from SimBenchData Package
Comment: incomplete imputation of missing values with LEA impute() function
Answer: Expected memory usage for analyzing large single-cell seq datasets (> 450,000 ce
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