Showing : rnaseq • reset
2
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How do I set up a contrast matrix in edgeR with makeContrasts, when a relevant level was dropped?
edgeR RNASeq
updated 8 days ago by 42k • written 8 days ago by • 0
1
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2
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56
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Unable to use ensembldb's "ensDbFromGff()" function on .gff file from NCBI
ensembldb RNASeq
9 days ago • updated 8 days ago Torkel • 0
3
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4
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127
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GEO + RNA-seq. Total Newbie.
RNASeqData RNASeq GEO RNASeqR HELP
12 days ago • updated 11 days ago hgalmoore • 0
0
votes
1
reply
86
views
Limma Voom Design and Contrast Matrix- Can my parameter also be a factor?
RNASeqRData limma RNASeq RNASeqR
updated 13 days ago by 42k • written 14 days ago by • 0
0
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2
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90
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voom-limma workflow for RNAseq samples with very different numbers of counts
voom limma RNASeq
17 days ago • updated 16 days ago annadv • 0
1
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3
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77
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DEGpatterns and functional analysis of clusters
DESeq2 RNASeq DEGreport
updated 4 weeks ago by 2.7k • written 4 weeks ago by • 0
0
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2
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115
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edgeR - Chapter 4.8 Time Course RNAseq experiments
edgeR TimeCourse RNASeq
updated 29 days ago by 42k • written 4 weeks ago by ▴ 10
0
votes
1
reply
48
views
How to analyze ribosome profiling data in the form of a 2x2x2 experiment using DESeq2
DESeq2 RiboSeq RNASeq
updated 4 weeks ago by 32k • written 4 weeks ago by • 0
0
votes
3
replies
118
views
ComBat Normalisation - data is integers and some floats, confused?!
combat rnaseq combatnormalisation jeffleek sva
updated 5 weeks ago by 2.7k • written 5 weeks ago by • 0
1
vote
1
reply
91
views
read nanopore Fastq file
NanoporeRNASeq RNASeq
updated 5 weeks ago by 56k • written 5 weeks ago by • 0
4
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9
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306
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Using edgeR and a spike-in to calculate absolute abundance
edgeR SpikeIn RNASeq
6 weeks ago • updated 4 weeks ago robert.chen • 0
2
votes
2
replies
105
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Question: Error when running QoRTs for JunctionSeq
DEXSeq JunctionSeq RNAseq QoRTs
8 weeks ago • updated 5 weeks ago n.tear ▴ 10
1
vote
0
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64
views
Design Matrix for multiple variables in Edge R
designmatrix DifferentialExpression edgeR RNAseq
8 weeks ago • updated 7 weeks ago nageshprabhu.k ▴ 10
2
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2
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97
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Preprocessing Issue
sva RNASeq Preprocessing Normalization BatchEffect
updated 8 weeks ago by ▴ 570 • written 8 weeks ago by • 0
0
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0
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41
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Circular RNA
CircularRNA RNASeq RNAseq123
9 weeks ago rpokhre2 • 0
0
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4
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159
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DEseq2: setting up the correct contrast.
DESeq2 RNASeq
updated 10 weeks ago by ▴ 680 • written 10 weeks ago by • 0
1
vote
1
reply
88
views
No result from plotPCA()
DESeq2 RNASeq plotpca
updated 10 weeks ago by 32k • written 10 weeks ago by • 0
1
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0
replies
51
views
Saving the results of the topGO package as an R object (rda/rds file).
RNASeq GO topGO Pathways
10 weeks ago Ben ▴ 20
0
votes
2
replies
148
views
Design Matrix for DESeq2 or EdgeR
edgeR DESeq2 RNASeq
updated 12 weeks ago by 32k • written 12 weeks ago by • 0
0
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1
reply
81
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Using Deseq2 for RNA-seq analysis of 4 different groups of cells
DESeq2 RNASeq
updated 3 months ago by ▴ 570 • written 3 months ago by • 0
0
votes
5
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173
views
How to remove X & Y chromosome genes from RNAseq data
DESeq2 RNASeq
updated 3 months ago by • 0 • written 3 months ago by • 0
3
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15
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417
views
How to ellipse a subset of data PCA biplot?
biplot PCA RNASeq PCAtools
updated 3 months ago by 2.7k • written 3 months ago by ▴ 10
3
votes
9
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4.5k
views
merge fastq.gz in R? (or in Windows?)
rnaseq bioconductor fastq
updated 4 months ago by • 0 • written 5.7 years ago by • 0
0
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1
reply
116
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DESeq2 with three factor experimental design
DESeq2 RNASeq
updated 4 months ago by 32k • written 4 months ago by • 0
2
votes
2
replies
149
views
Addressing the batch effect in multifactor experiment
edgeR BatchEffect RNASeq
updated 4 months ago by ▴ 270 • written 4 months ago by • 0
0
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2
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108
views
How well does "Trinity-Differential-Expression" work on normalized raw counts without RSEM abundance of estimation
Trinity DifferentialExpression RSEM RNAseq edgeR
4 months ago harelarik ▴ 50
0
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1
reply
115
views
Perform a biplot from pcaData and coldata in DESeq2, maybe PCAtools?
PCAtools biplot DESeq2 RNASeq PCA
updated 4 months ago by 2.7k • written 4 months ago by • 0
0
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3
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167
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Pearson correlation between gene expression and phenotype
edgeR RNASeq
updated 4 months ago by 42k • written 4 months ago by • 0
2
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3
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189
views
Normalization for within-sample gene correlation
edgeR Normalization DESeq2 tpm RNASeq
updated 4 months ago by 42k • written 4 months ago by ▴ 40
3
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2
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101
views
lfcShrink function for different comparison
DESeq2 RNASeq
5 months ago bi.mi • 0
1
vote
1
reply
95
views
DESeq2 batch effects
BatchEffect DESeq2 RNASeq
updated 5 months ago by 32k • written 5 months ago by ▴ 40
0
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4
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142
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DESeq2: Model matrix problem with 30 samples
DESeq2 RNAseq
5 months ago dagurim • 0
2
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1
reply
75
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How to extract top DEG and their sample values
DESeq2 RNASeq
updated 5 months ago by 2.7k • written 5 months ago by • 0
0
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2
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150
views
Why counts to tpm gives different values compared to tpm from kallisto?
rnaseq counts tpm GenomicFeatures kallisto
updated 5 months ago by 32k • written 5 months ago by • 0
2
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3
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302
views
What lengths are used to calculate TPM in "scater" package
scater calculateTPM RNAseq
updated 5 months ago by ★ 26k • written 6 months ago by ▴ 30
0
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0
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141
views
Job: PhD position in Developmental Neurobiology and Bioinformatics
rnaseq neurobiology tcga Job
5 months ago Laurent Gatto 1.5k
3
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4
replies
225
views
AnnotationData package for Affymetrix HT MG-430 PM Array Plate
RNAseq Affymetrix Mouse
updated 6 months ago by ★ 2.9k • written 6 months ago by • 0
0
votes
1
reply
158
views
non-native GO annotation cannot be successfully introduced into Goseq
goseq rnaseq r
updated 6 months ago by 56k • written 6 months ago by • 0
6
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5
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216
views
Calculating standard deviation for a few genes using RNAseq data
edger RNAseq
updated 7 months ago by 13k • written 7 months ago by • 0
3
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6
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151
views
EdgeR design matrix with 3 factors
edgeR glm RNAseq
updated 7 months ago by 56k • written 7 months ago by • 0
0
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2
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184
views
deseq2 + filtering low counts with noiseq function
deseq2 noiseq lowcounts rnaseq
updated 7 months ago by 32k • written 7 months ago by • 0
1
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7
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138
views
How to get multi-factor Deseq LRT test log P values for a particular condition
Deseq2 LRT Factors RNAseq
7 months ago aishu.jp ▴ 20
5
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8
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247
views
Sort decreasing only numeric columns (more than one) in a dataframe with character and numeric column
sort R RNAseq character numeric
updated 7 months ago by ▴ 60 • written 7 months ago by ▴ 10
0
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2
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202
views
CPM function in EDGER
edger cpm rnaseq
7 months ago francesca3 • 0
0
votes
1
reply
114
views
How to describe LRT test condition for time series RNA-seq data of 2 varieties
deseq2 LRT RNAseq condition
updated 8 months ago by 32k • written 8 months ago by ▴ 20
1
vote
1
reply
146
views
Can I add raw counts for duplicated genes?
DESeq2 RNAseq
updated 8 months ago by 32k • written 8 months ago by • 0
7
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11
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207
views
Is there any model in EdgeR that is close to nested ANOVA?
edger rnaseq
updated 8 months ago by 42k • written 8 months ago by • 0
2
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2
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151
views
edgeR batch effect correction for unevenly distributed groups
rnaseq edgeR batch effect
updated 8 months ago by 42k • written 8 months ago by • 0
0
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1
reply
122
views
StringTie output as Ballgown input
ballgown StringTie galaxy rnaseq
updated 8 months ago by 2.7k • written 8 months ago by • 0
0
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0
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107
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EDASeq: is it possible to normalize within lanes for more than one covariate?
EDASeq normalization GC length RNASeq
8 months ago abf ▴ 30
1,059 results • Page 1 of 22
Recent ...
Replies
Answer: DepMap copy number by Laurent Gatto 1.5k
Hi Danny - sorry for the delay in answering, I hadn't set `depmap` as a tag yet. Yes, that bug has been fixed in the devel version.
Answer: High fold change reported for comparison of samples with zero values in all samp by James W. MacDonald 56k
The universal recommendation is to remove all genes with consistently low (or all zero) expression values prior to doing any modeling. It i…
Comment: Sample quality weights for RNA-seq by Naomi Altman ★ 6.0k
Thanks Michael. I'll try that. (Limma folks, I'd still love to hear from you.)
Answer: Installation error if message implemented in .Rprofile by Mike Smith ★ 4.9k
A similar issue has been reported recently for rhdf5filters (https://github.com/grimbough/rhdf5filters/issues/11) and rhdf5 (https://github…
Comment: Couldn't load org.Hs.eg.db by Xulei Huo • 0
That does not work, i have tried it.
Votes
Answer: TargetsFile. Where it is?
Answer: TargetsFile. Where it is?
Comment: TargetsFile. Where it is?
Comment: Using DESeq2 to identify changing transcriptional activity in a metagenome
Answer: .onLoad failed in loadNamespace() for 'org.Hs.eg.db'
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