Showing : RnaSeq • reset
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Multi-factor Analysis in DeSEQ2
tximport R tximportData RNASeq DESeq2
updated 4.5 years ago by 43k • written 4.5 years ago by • 0
2
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1
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1.5k
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Salmon and DEseq2 - analysis of libraries saturated with ncRNAs
RNASeq Salmon DESeq2
updated 4.5 years ago by 43k • written 4.5 years ago by • 0
6
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6
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3.6k
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Weird output of biomaRt R package querying Ensembl IDs (hg19/grch37) to retrieve gene symbols
biomaRt annnotation RNASeq AnnotationDbi
4.5 years ago svlachavas ▴ 840
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2
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753
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Different P-Adjusted Values In DESeq2 for the same comparaison
RNASeq DESeq2
4.5 years ago fernandogs97 ▴ 10
1
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2
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912
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Technical reps
RNASeq DESeq2
updated 4.5 years ago by ★ 5.0k • written 4.5 years ago by • 0
3
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9
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8.1k
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LOC gene IDs for characterised genes in annotation files
Annotation RNAseq
updated 3.8 years ago by • 0 • written 4.5 years ago by • 0
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3
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1.5k
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DESeq2 ashr with and without reflevels generate different log2FoldChanges
DESeq2 RNASeq
updated 4.5 years ago by 43k • written 4.5 years ago by ▴ 10
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4
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1.6k
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Need help in running GO analysis
RNASeq R
4.5 years ago Rishav ▴ 20
4
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1
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3.8k
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Is it always preferable to recount library sizes of DGEList object in edgeR after filtering?
edgeR RnaSeqSampleSizeData RNAseq
updated 22 months ago by 53k • written 4.6 years ago by ▴ 60
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4
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1.6k
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subtracting or normalizing RNAseq reads when samples have contaminating reads
Normalization RNASeq contamination edgeR DESeq2
4.6 years ago Yuqia • 0
1
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6
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3.4k
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The correlation between normalized counts and TPM based on 2-factor analysis by DESeq2
DESeq2 RNASeq
4.6 years ago hequn • 0
1
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3
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3.2k
views
Mapping EntrezId to Ensembl IDs returns NA for pseudogenes and snoRNA
RNASeqData RNASeq RNASeqR
4.6 years ago dantasezequiel1 • 0
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2
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3.5k
views
How do I set up a contrast matrix in edgeR with makeContrasts, when a relevant level was dropped?
edgeR RNASeq
updated 4.6 years ago by 53k • written 4.6 years ago by • 0
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2
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1.6k
views
Unable to use ensembldb's "ensDbFromGff()" function on .gff file from NCBI
ensembldb RNASeq
4.6 years ago Torkel • 0
3
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4
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2.2k
views
GEO + RNA-seq. Total Newbie.
RNASeqData RNASeq GEO RNASeqR HELP
4.6 years ago hgalmoore • 0
0
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1
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1.2k
views
Limma Voom Design and Contrast Matrix- Can my parameter also be a factor?
RNASeqRData limma RNASeq RNASeqR
updated 4.6 years ago by 53k • written 4.6 years ago by • 0
0
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2
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1.4k
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voom-limma workflow for RNAseq samples with very different numbers of counts
voom limma RNASeq
4.6 years ago annadv • 0
2
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5
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5.1k
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DEGpatterns and functional analysis of clusters
DESeq2 RNASeq DEGreport
updated 3.0 years ago by 43k • written 4.7 years ago by ▴ 10
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2
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1.3k
views
edgeR - Chapter 4.8 Time Course RNAseq experiments
edgeR TimeCourse RNASeq
updated 4.7 years ago by 53k • written 4.7 years ago by ▴ 10
0
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1
reply
984
views
How to analyze ribosome profiling data in the form of a 2x2x2 experiment using DESeq2
DESeq2 RiboSeq RNASeq
updated 4.7 years ago by 43k • written 4.7 years ago by • 0
1
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4
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3.7k
views
ComBat Normalisation - data is integers and some floats, confused?!
combat rnaseq combatnormalisation jeffleek sva
updated 2.1 years ago by • 0 • written 4.7 years ago by • 0
1
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1
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1.9k
views
read nanopore Fastq file
NanoporeRNASeq RNASeq
updated 4.7 years ago by 68k • written 4.7 years ago by • 0
7
votes
12
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6.0k
views
Using edgeR and a spike-in to calculate absolute abundance
edgeR SpikeIn RNASeq
updated 2.1 years ago by • 0 • written 4.7 years ago by • 0
2
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2
replies
1.7k
views
Question: Error when running QoRTs for JunctionSeq
DEXSeq JunctionSeq RNAseq QoRTs
4.8 years ago • updated 4.7 years ago n.tear ▴ 20
1
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0
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986
views
Design Matrix for multiple variables in Edge R
designmatrix DifferentialExpression edgeR RNAseq
4.8 years ago nageshprabhu.k ▴ 10
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2
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1.6k
views
Preprocessing Issue
sva RNASeq Preprocessing Normalization BatchEffect
updated 4.8 years ago by ★ 5.0k • written 4.8 years ago by • 0
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0
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908
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Circular RNA
CircularRNA RNASeq RNAseq123
4.8 years ago rpokhre2 • 0
0
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4
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2.3k
views
DEseq2: setting up the correct contrast.
DESeq2 RNASeq
updated 4.8 years ago by ★ 1.4k • written 4.8 years ago by • 0
1
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1
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1.3k
views
No result from plotPCA()
DESeq2 RNASeq plotpca
updated 4.8 years ago by 43k • written 4.8 years ago by • 0
2
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0
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1.5k
views
Saving the results of the topGO package as an R object (rda/rds file).
RNASeq GO topGO Pathways
4.8 years ago Ben ▴ 50
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2
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1.1k
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Design Matrix for DESeq2 or EdgeR
edgeR DESeq2 RNASeq
updated 4.8 years ago by 43k • written 4.8 years ago by • 0
0
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1
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659
views
Using Deseq2 for RNA-seq analysis of 4 different groups of cells
DESeq2 RNASeq
updated 4.8 years ago by ★ 5.0k • written 4.8 years ago by • 0
2
votes
8
replies
4.2k
views
How to remove X & Y chromosome genes from RNAseq data
DESeq2 RNASeq
updated 23 months ago by • 0 • written 4.9 years ago by ▴ 20
3
votes
15
replies
4.5k
views
How to ellipse a subset of data PCA biplot?
biplot PCA RNASeq PCAtools
updated 4.9 years ago by ★ 4.0k • written 4.9 years ago by ▴ 10
3
votes
9
replies
11k
views
merge fastq.gz in R? (or in Windows?)
rnaseq bioconductor fastq
updated 4.9 years ago by • 0 • written 10.3 years ago by • 0
0
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1
reply
855
views
DESeq2 with three factor experimental design
DESeq2 RNASeq
updated 4.9 years ago by 43k • written 4.9 years ago by • 0
2
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2
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1.4k
views
Addressing the batch effect in multifactor experiment
edgeR BatchEffect RNASeq
updated 5.0 years ago by ▴ 360 • written 5.0 years ago by ▴ 10
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2
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2.0k
views
How well does "Trinity-Differential-Expression" work on normalized raw counts without RSEM abundance of estimation
Trinity DifferentialExpression RSEM RNAseq edgeR
5.0 years ago harelarik ▴ 60
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1
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2.5k
views
Perform a biplot from pcaData and coldata in DESeq2, maybe PCAtools?
PCAtools biplot DESeq2 RNASeq PCA
updated 5.0 years ago by ★ 4.0k • written 5.0 years ago by ▴ 30
0
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3
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3.1k
views
Pearson correlation between gene expression and phenotype
edgeR RNASeq
updated 5.0 years ago by 53k • written 5.0 years ago by ▴ 10
2
votes
3
replies
3.0k
views
Normalization for within-sample gene correlation
edgeR Normalization DESeq2 tpm RNASeq
updated 5.0 years ago by 53k • written 5.0 years ago by ▴ 100
15
votes
3
replies
2.4k
views
lfcShrink function for different comparison
DESeq2 RNASeq
updated 3.8 years ago by ▴ 30 • written 5.0 years ago by ▴ 90
1
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1
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1.9k
views
DESeq2 batch effects
BatchEffect DESeq2 RNASeq
updated 5.0 years ago by 43k • written 5.0 years ago by ▴ 50
0
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4
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1.4k
views
DESeq2: Model matrix problem with 30 samples
DESeq2 RNAseq
5.0 years ago dagurim • 0
2
votes
1
reply
999
views
How to extract top DEG and their sample values
DESeq2 RNASeq
updated 5.0 years ago by ★ 4.0k • written 5.0 years ago by ▴ 30
0
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2
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4.2k
views
Why counts to tpm gives different values compared to tpm from kallisto?
rnaseq counts tpm GenomicFeatures kallisto
updated 5.1 years ago by 43k • written 5.1 years ago by • 0
3
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3
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3.2k
views
What lengths are used to calculate TPM in "scater" package
scater calculateTPM RNAseq
updated 5.1 years ago by ★ 29k • written 5.1 years ago by ▴ 60
0
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0
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1.3k
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Job: PhD position in Developmental Neurobiology and Bioinformatics
rnaseq neurobiology tcga Job
5.1 years ago Laurent Gatto 1.6k
3
votes
4
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2.2k
views
AnnotationData package for Affymetrix HT MG-430 PM Array Plate
RNAseq Affymetrix Mouse
updated 5.1 years ago by ★ 4.1k • written 5.1 years ago by • 0
0
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1
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1.4k
views
non-native GO annotation cannot be successfully introduced into Goseq
goseq rnaseq r
updated 5.1 years ago by 68k • written 5.1 years ago by • 0
1,409 results • Page 8 of 29
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Comment: Alternative to BrainArray custom CDF packages for Affymetrix chips? by Stephen Piccolo ▴ 600
Thank you!
Answer: Alternative to BrainArray custom CDF packages for Affymetrix chips? by Guido Hooiveld ★ 4.1k
It seems that through the Internet Archive these files can be obtained: https://web.archive.org/web/20240710102334/http://brainarray.mbni.…
Comment: Getting a large intercept with DESeq2 by Denise • 0
Hi, Thank you very much, James and Michael, for getting back to me! I noticed the large intercept when plotting the coefficients returned …
Comment: Error installing Seqinfo by shepherl 4.2k
Yes and we are working on getting the updated windows binaries distributed asap! We are hopeful by the end of this week
Comment: APAlyzer by shepherl 4.2k
We apologize for their unresponsiveness; you could try posting your question here to see if anyone in the community could assist in the me…
Votes
Comment: Error installing Seqinfo
Answer: replace cat with message in glmTreat when lfc = 0
Answer: replace cat with message in glmTreat when lfc = 0
Comment: Issues with downloading biomaRt - SeqInfo and S4 Vectors
Answer: Issues with downloading biomaRt - SeqInfo and S4 Vectors
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