Showing : RNAseq • reset
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DESeq2 Multi-factor design not full rank
RNASeq DESeq2
updated 1 minute ago by 33k • written 23 minutes ago by • 0
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1
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23
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Technical reps
RNASeq DESeq2
updated 3 hours ago by 33k • written 3 hours ago by • 0
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45
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Salmon and DEseq2 - analysis of libraries saturated with ncRNAs
RNASeq Salmon DESeq2
2 days ago Mikołaj • 0
3
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4
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102
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LOC gene IDs for characterised genes in annotation files
Annotation RNAseq
5 days ago • updated 4 days ago Chris • 0
0
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3
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99
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DESeq2 ashr with and without reflevels generate different log2FoldChanges
DESeq2 RNASeq
updated 4 days ago by 33k • written 8 days ago by ▴ 10
1
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4
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150
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Need help in running GO analysis
RNASeq R
10 days ago • updated 8 days ago Rishav ▴ 10
2
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2
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93
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Is it always preferable to recount library sizes of DGEList object in edgeR after filtering?
edgeR RnaSeqSampleSizeData RNAseq
updated 14 days ago by 42k • written 15 days ago by • 0
0
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4
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116
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subtracting or normalizing RNAseq reads when samples have contaminating reads
Normalization RNASeq contamination edgeR DESeq2
19 days ago • updated 18 days ago Yuqia • 0
1
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6
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174
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The correlation between normalized counts and TPM based on 2-factor analysis by DESeq2
DESeq2 RNASeq
25 days ago hequn • 0
1
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3
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167
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Mapping EntrezId to Ensembl IDs returns NA for pseudogenes and snoRNA
RNASeqData RNASeq RNASeqR
27 days ago dantasezequiel1 • 0
2
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2
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119
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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 5 weeks ago by 42k • written 5 weeks ago by • 0
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2
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97
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Unable to use ensembldb's "ensDbFromGff()" function on .gff file from NCBI
ensembldb RNASeq
5 weeks ago Torkel • 0
3
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4
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171
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GEO + RNA-seq. Total Newbie.
RNASeqData RNASeq GEO RNASeqR HELP
6 weeks ago hgalmoore • 0
0
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1
reply
116
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Limma Voom Design and Contrast Matrix- Can my parameter also be a factor?
RNASeqRData limma RNASeq RNASeqR
updated 6 weeks ago by 42k • written 6 weeks ago by • 0
0
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2
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120
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voom-limma workflow for RNAseq samples with very different numbers of counts
voom limma RNASeq
7 weeks ago • updated 6 weeks ago annadv • 0
1
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3
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113
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DEGpatterns and functional analysis of clusters
DESeq2 RNASeq DEGreport
updated 8 weeks ago by 2.9k • written 8 weeks ago by • 0
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2
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145
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edgeR - Chapter 4.8 Time Course RNAseq experiments
edgeR TimeCourse RNASeq
updated 8 weeks ago by 42k • written 9 weeks ago by ▴ 10
0
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1
reply
61
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How to analyze ribosome profiling data in the form of a 2x2x2 experiment using DESeq2
DESeq2 RiboSeq RNASeq
updated 9 weeks ago by 33k • written 9 weeks ago by • 0
0
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3
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151
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ComBat Normalisation - data is integers and some floats, confused?!
combat rnaseq combatnormalisation jeffleek sva
updated 9 weeks ago by 2.9k • written 9 weeks ago by • 0
1
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1
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109
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read nanopore Fastq file
NanoporeRNASeq RNASeq
updated 10 weeks ago by 56k • written 10 weeks ago by • 0
4
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9
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365
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Using edgeR and a spike-in to calculate absolute abundance
edgeR SpikeIn RNASeq
11 weeks ago • updated 9 weeks ago robert.chen • 0
2
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2
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136
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Question: Error when running QoRTs for JunctionSeq
DEXSeq JunctionSeq RNAseq QoRTs
12 weeks ago • updated 9 weeks ago n.tear ▴ 10
1
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0
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75
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Design Matrix for multiple variables in Edge R
designmatrix DifferentialExpression edgeR RNAseq
12 weeks ago nageshprabhu.k ▴ 10
2
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2
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129
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Preprocessing Issue
sva RNASeq Preprocessing Normalization BatchEffect
updated 3 months ago by ▴ 640 • written 3 months ago by • 0
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0
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55
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Circular RNA
CircularRNA RNASeq RNAseq123
3 months ago rpokhre2 • 0
0
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4
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190
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DEseq2: setting up the correct contrast.
DESeq2 RNASeq
updated 3 months ago by ▴ 740 • written 3 months ago by • 0
1
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1
reply
105
views
No result from plotPCA()
DESeq2 RNASeq plotpca
updated 3 months ago by 33k • written 3 months ago by • 0
1
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0
replies
64
views
Saving the results of the topGO package as an R object (rda/rds file).
RNASeq GO topGO Pathways
3 months ago Ben ▴ 20
0
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2
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170
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Design Matrix for DESeq2 or EdgeR
edgeR DESeq2 RNASeq
updated 3 months ago by 33k • written 4 months ago by • 0
0
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1
reply
97
views
Using Deseq2 for RNA-seq analysis of 4 different groups of cells
DESeq2 RNASeq
updated 4 months ago by ▴ 640 • written 4 months ago by • 0
0
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5
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195
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How to remove X & Y chromosome genes from RNAseq data
DESeq2 RNASeq
updated 4 months ago by • 0 • written 4 months ago by • 0
3
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15
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498
views
How to ellipse a subset of data PCA biplot?
biplot PCA RNASeq PCAtools
updated 5 months ago by 2.9k • written 5 months ago by ▴ 10
3
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9
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4.6k
views
merge fastq.gz in R? (or in Windows?)
rnaseq bioconductor fastq
updated 5 months ago by • 0 • written 5.8 years ago by • 0
0
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1
reply
133
views
DESeq2 with three factor experimental design
DESeq2 RNASeq
updated 5 months ago by 33k • written 5 months ago by • 0
2
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2
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168
views
Addressing the batch effect in multifactor experiment
edgeR BatchEffect RNASeq
updated 5 months ago by ▴ 270 • written 5 months ago by • 0
0
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2
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135
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How well does "Trinity-Differential-Expression" work on normalized raw counts without RSEM abundance of estimation
Trinity DifferentialExpression RSEM RNAseq edgeR
5 months ago harelarik ▴ 50
0
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1
reply
143
views
Perform a biplot from pcaData and coldata in DESeq2, maybe PCAtools?
PCAtools biplot DESeq2 RNASeq PCA
updated 5 months ago by 2.9k • written 5 months ago by • 0
0
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3
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195
views
Pearson correlation between gene expression and phenotype
edgeR RNASeq
updated 5 months ago by 42k • written 6 months ago by • 0
2
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3
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221
views
Normalization for within-sample gene correlation
edgeR Normalization DESeq2 tpm RNASeq
updated 5 months ago by 42k • written 6 months ago by ▴ 40
3
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2
replies
119
views
lfcShrink function for different comparison
DESeq2 RNASeq
6 months ago bi.mi • 0
1
vote
1
reply
113
views
DESeq2 batch effects
BatchEffect DESeq2 RNASeq
updated 6 months ago by 33k • written 6 months ago by ▴ 40
0
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4
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170
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DESeq2: Model matrix problem with 30 samples
DESeq2 RNAseq
6 months ago dagurim • 0
2
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1
reply
86
views
How to extract top DEG and their sample values
DESeq2 RNASeq
updated 6 months ago by 2.9k • written 6 months ago by • 0
0
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2
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175
views
Why counts to tpm gives different values compared to tpm from kallisto?
rnaseq counts tpm GenomicFeatures kallisto
updated 6 months ago by 33k • written 6 months ago by • 0
2
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3
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346
views
What lengths are used to calculate TPM in "scater" package
scater calculateTPM RNAseq
updated 6 months ago by ★ 26k • written 7 months ago by ▴ 40
0
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0
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163
views
Job: PhD position in Developmental Neurobiology and Bioinformatics
rnaseq neurobiology tcga Job
6 months ago Laurent Gatto 1.5k
3
votes
4
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253
views
AnnotationData package for Affymetrix HT MG-430 PM Array Plate
RNAseq Affymetrix Mouse
updated 7 months ago by ★ 2.9k • written 7 months ago by • 0
0
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1
reply
179
views
non-native GO annotation cannot be successfully introduced into Goseq
goseq rnaseq r
updated 7 months ago by 56k • written 7 months ago by • 0
6
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5
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255
views
Calculating standard deviation for a few genes using RNAseq data
edger RNAseq
updated 8 months ago by 13k • written 8 months ago by • 0
3
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6
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172
views
EdgeR design matrix with 3 factors
edgeR glm RNAseq
updated 8 months ago by 56k • written 8 months ago by • 0
50 results • Page 1 of 1
Recent ...
Replies
Comment: phenotypic table for DESeqDataSetFromHTSeqCount by Michael Love 33k
Oh sorry I didn't see any code including a `directory` argument in your post. Then to debug do: ``` file.exists(file.path(directory, samp…
Comment: phenotypic table for DESeqDataSetFromHTSeqCount by rbenel ▴ 20
The vector contains just `FALSE`... So where is the `directory` parameter set to read files from? Currently I have `directory` set to a t…
Comment: `aperm`, `realize`, `writeHDF5Array`, and `ReshapedHDF5Array` are block size awa by Koki • 0
Ok, I got the gist of it. If I have the same situation of the previous case (https://support.bioconductor.org/p/9136736/), where I have to…
Answer: DESeq2 Design matrix by Michael Love 33k
Usually one would use a single design and extract comparisons. With a complex design, you should partner with someone familiar with linear …
Comment: `aperm`, `realize`, `writeHDF5Array`, and `ReshapedHDF5Array` are block size awa by Hervé Pagès 14k
> For example, the following codes use a combination of delayed operation and block-processed operation but the code as a whole does not ex…
Votes
Answer: erorr in normalization with DiffBind: pv$binding[, colnum] <- pv$peaks[[i]]$RPKM
Answer: phenotypic table for DESeqDataSetFromHTSeqCount
Comment: `aperm`, `realize`, `writeHDF5Array`, and `ReshapedHDF5Array` are block size awa
Answer: Error: C stack usage of HDF5Array
Answer: "dim<-" against on-disk arrays
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