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4
votes
1
answer
111
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1
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DESeq multiple factor question
R differential-expression rna-seq sequencing written 9 days ago by jdhindsa1999 • 0 • updated 9 days ago by Carlo Yague ♦ 5.7k
1
vote
0
answers
288
views
0
answers
Should I integrate datasets between conditions if I am doing differential expression analysis between the conditions?
batch-effect differential-expression rna-seq written 7 weeks ago by townsendae • 0
3
votes
1
answer
393
views
1
answer
Differential Gene Expression Analysis with low biological replicates
R ngs differential-expression rna-seq written 9 months ago by spriyansh29 • 30 • updated 8 months ago by Biostar ♦♦ 20
4
votes
3
answers
1.9k
views
5 follow
3
answers
Go Analysis From De-Genes
differential-expression go written 7.0 years ago by Phil S. • 660 • updated 8 months ago by Biostar ♦♦ 20
0
votes
0
answers
712
views
0
answers
Seurat integrated analysis - methods for cell-type specific responses
single-cell differential-expression rna-seq written 10 months ago by jomo018 • 610
0
votes
0
answers
386
views
0
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Filtering criteria for selecting DEGs from Monocle3 regression analysis with categorical terms
differential-expression rna-seq monocle written 14 months ago by gundalav • 310
4
votes
1
answer
1.3k
views
1
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Differential expression tool that can take TPM as input?
differential-expression tpm rna-seq written 14 months ago by Tye Kahn • 10 • updated 14 months ago by ATpoint ♦ 46k
0
votes
1
answer
579
views
1
answer
Identifiyng mutual trends between treatments
differential-expression deseq2 rna-seq statistics written 2.2 years ago by uriamo • 0 • updated 2.2 years ago by kristoffer.vittingseerup • 3.5k
2
votes
1
answer
432
views
1
answer
Is it correct to pool transcriptomes coming from different experiment for DE analysis?
differential-expression rna-seq written 2.5 years ago by keepclam • 10 • updated 2.5 years ago by WouterDeCoster ♦ 45k
1
vote
0
answers
1.4k
views
0
answers
FPKM values from SE vs. PE RNA-Seq libraries
gene fpkm differential-expression rna-seq written 3.7 years ago by s_herrera • 10 • updated 2.6 years ago by Biostar ♦♦ 20
0
votes
1
answer
785
views
1
answer
Differential Expression from Quantile-Norm Data
differential-expression rna-seq written 2.8 years ago by matthew.m.hernandez • 30 • updated 2.8 years ago by Hussain Ather • 950
13
votes
4
answers
2.1k
views
5 follow
4
answers
Is it appropriate to assume genes of similar expression level also have similar variance?
differential-expression deseq written 3.1 years ago by -_- • 880 • updated 3.1 years ago by Santosh Anand ♦ 5.3k
11
votes
2
answers
9.7k
views
9 follow
2
answers
Why Cannot Limma Package Do Differential Expression Between Two Samples Without Replication?
replicates differential-expression limma affymetrix written 7.7 years ago by shangzhong0619 • 20 • updated 3.1 years ago by Biostar ♦♦ 20
14
votes
1
answer
1.3k
views
8 follow
1
answer
Intersection of multiple methods for RNA-Seq differential expression: conservative or crazy?
differential-expression rna-seq written 3.3 years ago by Adamc • 640 • updated 3.3 years ago by Friederike ♦ 6.7k
1
vote
1
answer
1.6k
views
1
answer
Transcripts with beta close to zero are considered differentially expressed in a likelihood-ratio test in sleuth
sleuth differential-expression rna-seq written 3.5 years ago by elsoja • 130
0
votes
2
answers
1.8k
views
2
answers
differential expression based on multiple biological repeats
rpkm differential-expression rna-seq written 6.4 years ago by Whetting • 1.5k • updated 3.5 years ago by KVC_bioinfo • 520
2
votes
1
answer
2.1k
views
1
answer
Multiple group model matrix in rna-seq DE analysis
differential-expression rna-seq model-matrix written 3.6 years ago by andrea.rubiop88 • 0 • updated 3.6 years ago by Devon Ryan ♦ 98k
0
votes
0
answers
1.7k
views
0
answers
MA plot from Differential Expression between One Sample vs another
R bioconductor differential-expression rna-seq written 3.7 years ago by Ron • 1.0k
8
votes
1
answer
3.8k
views
6 follow
1
answer
Select top differentially expressed genes based on both p-value and fold-change
differential-expression deseq2 rna-seq written 3.8 years ago by RT • 350 • updated 3.8 years ago by Santosh Anand ♦ 5.3k
1
vote
1
answer
5.1k
views
5 follow
1
answer
De Genes And Isoforms?
ngs differential-expression rna-seq written 7.8 years ago by lzsph • 70 • updated 3.9 years ago by Biostar ♦♦ 20
16
votes
2
answers
1.2k
views
2
answers
Differences between Counts and FPKMS
next-gen differential-expression deseq rna-seq written 4.0 years ago by Ron • 1.0k • updated 4.0 years ago by Rob ♦ 4.6k
15
votes
3
answers
7.4k
views
11 follow
3
answers
Identifying De Novo Variants In Trio Data
gatk differential-expression variant written 8.7 years ago by Vivek • 2.5k • updated 4.4 years ago by daniel • 30
11
votes
2
answers
8.0k
views
5 follow
2
answers
How Do I Estimate The Number Of Rna-Seq Reads Needed To Detect Differential Expression?
reads differential-expression rna-seq written 7.3 years ago by scottdaniel25 • 30 • updated 4.6 years ago by Biostar ♦♦ 20
9
votes
2
answers
3.9k
views
2
answers
Limma calls all genes as differentially expressed - what am I doing wrong?
differential-expression limma rna-seq voom written 6.4 years ago by Amusement Pork • 60 • updated 6.4 years ago by Manvendra Singh • 2.1k
7
votes
0
answers
3.6k
views
0
answers
What's the real difference between these two types of methods for assessing differential expression?
differential-expression methods rna-seq written 6.4 years ago by Amusement Pork • 60
9
votes
4
answers
9.4k
views
9 follow
4
answers
Rna-Seq Data Normalization With Spike-In Using Deseq
R differential-expression bioinformatics written 7.5 years ago by ivivek_ngs • 5.1k • updated 6.6 years ago by Reza • 10
10
votes
1
answer
9.8k
views
8 follow
1
answer
Deseq Vs Edger..Filtering Read Counts.
deseq differential-expression tophat2 rna-seq rnaseq edger written 7.0 years ago by geek_y ♦ 11k • updated 6.7 years ago by bioinforupesh2009.au • 130
1
vote
3
answers
4.3k
views
3
answers
Best Workflow For Differential Expression Analysis Using De Novo Transcriptomes And Illumina Reads In 2014
differential-expression workflow alignment written 6.9 years ago by Birdman • 20 • updated 6.9 years ago by seidel ♦ 7.4k
3
votes
2
answers
6.5k
views
2
answers
Generating Counts Data From Fastq Sequence Files
fastq differential-expression counts rna-seq sequencing written 7.0 years ago by josph.sh • 0 • updated 7.0 years ago by Xingyu Yang • 260
2
votes
1
answer
6.5k
views
1
answer
Normalization And Differential Expression Analysis Of Mass Spectrometry Data
proteomics normalization differential-expression mass-spec R written 7.0 years ago by Ali • 140 • updated 7.0 years ago by Woa • 2.8k
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