Showing : RNASEQ • reset
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Complex design with paired and unpaired samples with edgeR RNA-seq DE analysis
edgeR RNASeq
20 hours ago Basti ▴ 150
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1
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85
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Creating the correct model to account for paired-samples (patient-effect) help needed!
edgeR limma rnaseq
updated 4 days ago by 33k • written 4 days ago by • 0
1
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1
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85
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DESeq2 for allele-specific expression with contrasts between conditions
DESeq2 AllelicImbalance edgeR RNASeq
updated 5 days ago by 33k • written 6 days ago by • 0
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8
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232
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DESeq2: Variable Importance
DESeq2 RNASeq
updated 9 days ago by 33k • written 11 days ago by • 0
2
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3
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104
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RNAseq : identical sample-sample distances after using limma::removeBatchEffect
DESeq2 RNASeq BatchEffect limma
updated 10 days ago by • 0 • written 13 days ago by • 0
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1
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88
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Query regarding WGCNA module formation
WGCNA RNAseq RNASeqData
updated 18 days ago by ▴ 640 • written 20 days ago by • 0
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34
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TCSeq input information
time RNAseq TCSeq
25 days ago curiousmind007 • 0
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5
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1.0k
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Error in stattest function
R rnaseq Ballgown
updated 26 days ago by • 0 • written 3.4 years ago by • 0
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1
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55
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Filtering DESeq2 results for | LFC | > 1 genes
RNAseq LFC DEseq
27 days ago ayy2110 • 0
4
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8
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247
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Interpreting ellipses in PCAtools for bulk RNAseq
ellipse RNAseq PCAtools
written 29 days ago by • 0
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2
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92
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Can't install KEGGprofile
KEGG RNASeq
updated 27 days ago by 57k • written 27 days ago by • 0
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1
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87
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Error in DESeqDataSetFromMatrix()
DESeq2 RNAseq
updated 28 days ago by 33k • written 28 days ago by • 0
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1
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76
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Extracting Go-enrichment and pathway analysis from phytozome annotation file
RNASeq GO
updated 28 days ago by 57k • written 29 days ago by • 0
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1
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100
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Multi-factor Analysis in DeSEQ2
tximport R tximportData RNASeq DESeq2
updated 4 weeks ago by 33k • written 4 weeks ago by • 0
2
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1
reply
129
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Salmon and DEseq2 - analysis of libraries saturated with ncRNAs
RNASeq Salmon DESeq2
updated 4 weeks ago by 33k • written 5 weeks ago by • 0
6
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6
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179
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Weird output of biomaRt R package querying Ensembl IDs (hg19/grch37) to retrieve gene symbols
biomaRt annnotation RNASeq AnnotationDbi
4 weeks ago svlachavas ▴ 780
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2
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113
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Different P-Adjusted Values In DESeq2 for the same comparaison
RNASeq DESeq2
4 weeks ago fernandogs97 • 0
0
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4
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122
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DESeq2 Multi-factor design not full rank
RNASeq DESeq2
5 weeks ago jehimi • 0
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2
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117
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Technical reps
RNASeq DESeq2
updated 5 weeks ago by ▴ 650 • written 5 weeks ago by • 0
3
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4
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173
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LOC gene IDs for characterised genes in annotation files
Annotation RNAseq
5 weeks ago Chris • 0
0
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3
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129
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DESeq2 ashr with and without reflevels generate different log2FoldChanges
DESeq2 RNASeq
updated 5 weeks ago by 33k • written 6 weeks ago by ▴ 10
1
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4
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199
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Need help in running GO analysis
RNASeq R
6 weeks ago Rishav ▴ 20
2
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2
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139
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Is it always preferable to recount library sizes of DGEList object in edgeR after filtering?
edgeR RnaSeqSampleSizeData RNAseq
updated 7 weeks ago by 43k • written 7 weeks ago by ▴ 20
0
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4
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163
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subtracting or normalizing RNAseq reads when samples have contaminating reads
Normalization RNASeq contamination edgeR DESeq2
7 weeks ago Yuqia • 0
1
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6
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230
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The correlation between normalized counts and TPM based on 2-factor analysis by DESeq2
DESeq2 RNASeq
8 weeks ago hequn • 0
1
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3
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217
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Mapping EntrezId to Ensembl IDs returns NA for pseudogenes and snoRNA
RNASeqData RNASeq RNASeqR
9 weeks ago dantasezequiel1 • 0
2
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2
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148
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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 10 weeks ago by 43k • written 11 weeks ago by • 0
1
vote
2
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128
views
Unable to use ensembldb's "ensDbFromGff()" function on .gff file from NCBI
ensembldb RNASeq
11 weeks ago • updated 10 weeks ago Torkel • 0
3
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4
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221
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GEO + RNA-seq. Total Newbie.
RNASeqData RNASeq GEO RNASeqR HELP
11 weeks ago hgalmoore • 0
0
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1
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147
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Limma Voom Design and Contrast Matrix- Can my parameter also be a factor?
RNASeqRData limma RNASeq RNASeqR
updated 11 weeks ago by 43k • written 11 weeks ago by • 0
0
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2
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147
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voom-limma workflow for RNAseq samples with very different numbers of counts
voom limma RNASeq
12 weeks ago annadv • 0
1
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3
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185
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DEGpatterns and functional analysis of clusters
DESeq2 RNASeq DEGreport
updated 3 months ago by 3.1k • written 3 months ago by • 0
0
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2
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173
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edgeR - Chapter 4.8 Time Course RNAseq experiments
edgeR TimeCourse RNASeq
updated 3 months ago by 43k • written 3 months ago by ▴ 10
0
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1
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82
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How to analyze ribosome profiling data in the form of a 2x2x2 experiment using DESeq2
DESeq2 RiboSeq RNASeq
updated 3 months ago by 33k • written 3 months ago by • 0
0
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3
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194
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ComBat Normalisation - data is integers and some floats, confused?!
combat rnaseq combatnormalisation jeffleek sva
updated 3 months ago by 3.1k • written 3 months ago by • 0
1
vote
1
reply
135
views
read nanopore Fastq file
NanoporeRNASeq RNASeq
updated 3 months ago by 57k • written 3 months ago by • 0
4
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9
replies
439
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Using edgeR and a spike-in to calculate absolute abundance
edgeR SpikeIn RNASeq
3 months ago robert.chen • 0
2
votes
2
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163
views
Question: Error when running QoRTs for JunctionSeq
DEXSeq JunctionSeq RNAseq QoRTs
4 months ago • updated 3 months ago n.tear ▴ 10
1
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0
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95
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Design Matrix for multiple variables in Edge R
designmatrix DifferentialExpression edgeR RNAseq
4 months ago nageshprabhu.k ▴ 10
2
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2
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160
views
Preprocessing Issue
sva RNASeq Preprocessing Normalization BatchEffect
updated 4 months ago by ▴ 650 • written 4 months ago by • 0
0
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0
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70
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Circular RNA
CircularRNA RNASeq RNAseq123
4 months ago rpokhre2 • 0
0
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4
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215
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DEseq2: setting up the correct contrast.
DESeq2 RNASeq
updated 4 months ago by ▴ 780 • written 4 months ago by • 0
1
vote
1
reply
126
views
No result from plotPCA()
DESeq2 RNASeq plotpca
updated 4 months ago by 33k • written 4 months ago by • 0
1
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0
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81
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Saving the results of the topGO package as an R object (rda/rds file).
RNASeq GO topGO Pathways
4 months ago Ben ▴ 20
0
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2
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200
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Design Matrix for DESeq2 or EdgeR
edgeR DESeq2 RNASeq
updated 5 months ago by 33k • written 5 months ago by • 0
0
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1
reply
113
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Using Deseq2 for RNA-seq analysis of 4 different groups of cells
DESeq2 RNASeq
updated 5 months ago by ▴ 650 • written 5 months ago by • 0
0
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5
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224
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How to remove X & Y chromosome genes from RNAseq data
DESeq2 RNASeq
updated 5 months ago by • 0 • written 5 months ago by • 0
3
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15
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580
views
How to ellipse a subset of data PCA biplot?
biplot PCA RNASeq PCAtools
updated 6 months ago by 3.1k • written 6 months ago by ▴ 10
3
votes
9
replies
4.7k
views
merge fastq.gz in R? (or in Windows?)
rnaseq bioconductor fastq
updated 6 months ago by • 0 • written 5.9 years ago by • 0
0
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1
reply
161
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DESeq2 with three factor experimental design
DESeq2 RNASeq
updated 6 months ago by 33k • written 6 months ago by • 0
50 results • Page 1 of 1
Recent ...
Replies
Comment: change text size in plotmd functtion by najib • 0
I mean the axis x and y and their number as well change the font to bold. also is it possible to store the produced graph as follow: p<- p…
Answer: change text size in plotmd functtion by Gordon Smyth 43k
Do you mean the text in the legend? Anyway, just make the dimensions of your graphics window smaller, then all points, labels and text in t…
Comment: Annotation using QSEA package by rtrivedi1 ▴ 10
Issue is fixed now !! Thanks Rakesh
Comment: Binding matrix created by DiffBind by sh.kazempour94 ▴ 10
Thank you for helping me figuring this out! The matrix from dba.peakset() seems to be the correct one. Thanks!
Comment: Annotation using QSEA package by James W. MacDonald 57k
OK. This is the part I meant about using an accessor. There is a function called `genome` that does what you have tried to do. It actually …
Votes
Comment: Annotation using QSEA package
Comment: Binding matrix created by DiffBind
Comment: Annotation using QSEA package
Answer: Annotation using QSEA package
Answer: lmFit, number of proteins
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