Showing : rnaseq • reset
0
Votes
2
Replies
85
Views
Design Matrix for DESeq2 or EdgeR
edgeR DESeq2 RNASeq
6 days ago kimmcl860 • 0 • updated 3 days ago Michael Love 31k
0
Votes
1
Reply
47
Views
Using Deseq2 for RNA-seq analysis of 4 different groups of cells
DESeq2 RNASeq
9 days ago yonatan • 0 • updated 9 days ago ATpoint • 390
0
Votes
5
Replies
131
Views
How to remove X & Y chromosome genes from RNAseq data
DESeq2 RNASeq
19 days ago Archit • 0 • updated 16 days ago Anubhav • 0
3
Votes
15
Replies
281
Views
How to ellipse a subset of data PCA biplot?
biplot PCA RNASeq PCAtools
5 weeks ago mschmidt • 10 • updated 4 weeks ago Kevin Blighe 2.3k
3
Votes
9
Replies
4.2k
Views
merge fastq.gz in R? (or in Windows?)
rnaseq bioconductor fastq
5.5 years ago mk.applebee • 0 • updated 5 weeks ago Rafael • 0
0
Votes
1
Reply
79
Views
DESeq2 with three factor experimental design
DESeq2 RNASeq
6 weeks ago microPhD • 0 • updated 6 weeks ago Michael Love 31k
2
Votes
2
Replies
114
Views
Addressing the batch effect in multifactor experiment
edgeR BatchEffect RNASeq
8 weeks ago anikng • 0 • updated 6 weeks ago SamGG • 250
0
Votes
2
Replies
75
Views
How well does "Trinity-Differential-Expression" work on normalized raw counts without RSEM abundance of estimation
Trinity DifferentialExpression RSEM RNAseq edgeR
7 weeks ago harelarik • 50
0
Votes
1
Reply
75
Views
Perform a biplot from pcaData and coldata in DESeq2, maybe PCAtools?
PCAtools biplot DESeq2 RNASeq PCA
8 weeks ago ecg1g15 • 0 • updated 8 weeks ago Kevin Blighe 2.3k
0
Votes
3
Replies
127
Views
Pearson correlation between gene expression and phenotype
edgeR RNASeq
9 weeks ago weichengz • 0 • updated 9 weeks ago Gordon Smyth 41k
2
Votes
3
Replies
141
Views
Normalization for within-sample gene correlation
edgeR Normalization DESeq2 tpm RNASeq
9 weeks ago tcalvo • 40 • updated 9 weeks ago Gordon Smyth 41k
3
Votes
2
Replies
75
Views
lfcShrink function for different comparison
DESeq2 RNASeq
10 weeks ago bi.mi • 0
1
Vote
1
Reply
67
Views
DESeq2 batch effects
BatchEffect DESeq2 RNASeq
10 weeks ago igor • 40 • updated 10 weeks ago Michael Love 31k
0
Votes
4
Replies
97
Views
DESeq2: Model matrix problem with 30 samples
DESeq2 RNAseq
11 weeks ago dagurim • 0
2
Votes
1
Reply
56
Views
How to extract top DEG and their sample values
DESeq2 RNASeq
11 weeks ago ecg1g15 • 0 • updated 11 weeks ago Kevin Blighe 2.3k
0
Votes
2
Replies
108
Views
Why counts to tpm gives different values compared to tpm from kallisto?
rnaseq counts tpm GenomicFeatures kallisto
12 weeks ago m93 • 0 • updated 12 weeks ago Michael Love 31k
2
Votes
3
Replies
226
Views
What lengths are used to calculate TPM in "scater" package
scater calculateTPM RNAseq
3 months ago Matan G. • 30 • updated 12 weeks ago Aaron Lun ♦ 26k
0
Votes
0
Replies
99
Views
Job: PhD position in Developmental Neurobiology and Bioinformatics
rnaseq neurobiology tcga Job
3 months ago Laurent Gatto 1.4k
3
Votes
4
Replies
154
Views
AnnotationData package for Affymetrix HT MG-430 PM Array Plate
RNAseq Affymetrix Mouse
3 months ago olrema • 0 • updated 3 months ago Guido Hooiveld ♦ 2.8k
0
Votes
1
Reply
119
Views
non-native GO annotation cannot be successfully introduced into Goseq
goseq rnaseq r
3 months ago citronxu • 0 • updated 3 months ago James W. MacDonald 56k
6
Votes
5
Replies
166
Views
Calculating standard deviation for a few genes using RNAseq data
edger RNAseq
4 months ago marhabaie • 0 • updated 4 months ago Steve Lianoglou 13k
3
Votes
6
Replies
122
Views
EdgeR design matrix with 3 factors
edgeR glm RNAseq
4 months ago jackiesalzbank • 0 • updated 4 months ago James W. MacDonald 56k
0
Votes
2
Replies
137
Views
deseq2 + filtering low counts with noiseq function
deseq2 noiseq lowcounts rnaseq
4 months ago andreia • 0 • updated 4 months ago Michael Love 31k
1
Vote
7
Replies
105
Views
How to get multi-factor Deseq LRT test log P values for a particular condition
Deseq2 LRT Factors RNAseq
4 months ago aishu.jp • 20
5
Votes
8
Replies
192
Views
Sort decreasing only numeric columns (more than one) in a dataframe with character and numeric column
sort R RNAseq character numeric
4 months ago camillab. • 10 • updated 4 months ago Ram • 60
0
Votes
2
Replies
135
Views
CPM function in EDGER
edger cpm rnaseq
4 months ago francesca3 • 0
0
Votes
1
Reply
87
Views
How to describe LRT test condition for time series RNA-seq data of 2 varieties
deseq2 LRT RNAseq condition
5 months ago aishu.jp • 20 • updated 5 months ago Michael Love 31k
1
Vote
1
Reply
91
Views
Can I add raw counts for duplicated genes?
DESeq2 RNAseq
5 months ago Nikolay Ivanov • 0 • updated 5 months ago Michael Love 31k
7
Votes
11
Replies
159
Views
Is there any model in EdgeR that is close to nested ANOVA?
edger rnaseq
5 months ago deeptiptl74 • 0 • updated 5 months ago Gordon Smyth 41k
2
Votes
2
Replies
120
Views
edgeR batch effect correction for unevenly distributed groups
rnaseq edgeR batch effect
5 months ago rebecca.lea.johnston • 0 • updated 5 months ago Gordon Smyth 41k
0
Votes
1
Reply
92
Views
StringTie output as Ballgown input
ballgown StringTie galaxy rnaseq
5 months ago lakshmi9c • 0 • updated 5 months ago Kevin Blighe 2.3k
0
Votes
0
Replies
77
Views
EDASeq: is it possible to normalize within lanes for more than one covariate?
EDASeq normalization GC length RNASeq
5 months ago abf • 30
1
Vote
5
Replies
123
Views
Spearman correlation for RNA SEQ data
deseq2 rnaseq statistic
6 months ago biom.andressa • 0 • updated 6 months ago Robert Castelo ♦ 2.6k
0
Votes
8
Replies
153
Views
Deseq2 weird values for Log2FC and pvalue.
deseq2 rnaseq r
6 months ago biom.andressa • 0 • updated 6 months ago Michael Love 31k
0
Votes
3
Replies
88
Views
DESeq2 Design Model and Results Function Set-Up - How to know if using the interaction term is appropriate?
deseq2 rnaseq
6 months ago gmchaput • 0 • updated 6 months ago Michael Love 31k
0
Votes
1
Reply
60
Views
How to obtain the specific genelists mentioned in the RNASeq DTU workflow?
rnaseqdtu RNASeq DEXSeq DESeq2
6 months ago debatosh das • 10 • updated 6 months ago Michael Love 31k
0
Votes
9
Replies
181
Views
ReactomePA error graph
r rnaseq bulk GO ReactomePA
7 months ago camillab. • 10
1
Vote
6
Replies
404
Views
Change fontsize/remove name of annotation ComplexHeatmap package
r rnaseq complexHeatmap annotation
7 months ago camillab. • 10 • updated 7 months ago Zuguang Gu • 210
0
Votes
1
Reply
81
Views
Coefficients not estimable voom Lima with multiple numeric covariate
r limma design rnaseq voom
7 months ago Will • 0 • updated 7 months ago Gordon Smyth 41k
0
Votes
0
Replies
347
Views
Job: Research software engineer at the de Duve Institute, UCLouvain (Brussels, Belgium)
software engineer RNASeq proteomics Job visualisation
7 months ago Laurent Gatto 1.4k
2
Votes
7
Replies
144
Views
Limma analysis with multiple variables
limma model.matrix de design rnaseq
7 months ago Will • 0 • updated 7 months ago Gordon Smyth 41k
4
Votes
14
Replies
223
Views
Application of quantro to RNASeq: I do not get the same results as are in the quantro paper supplement
quantro RNASeq
8 months ago raf4 • 20 • updated 7 months ago Stephanie Hicks • 80
2
Votes
1
Reply
129
Views
Cross-species analysis and normalization with DESeq2
normalization deseq2 across species rnaseq
7 months ago rmurray2050 • 0 • updated 7 months ago Michael Love 31k
1
Vote
8
Replies
129
Views
[Outlier Gene removal] - One sample with outlier counts for some genes
RNAseq DESeq2 outlier counts DE analysis
8 months ago DcL-A • 0 • updated 8 months ago Kevin Blighe 2.3k
1
Vote
2
Replies
78
Views
tximport from RSEM expected counts: is it possible to import from a table rather than a file?
tximport limma rnaseq
8 months ago Ahdee • 50 • updated 8 months ago Michael Love 31k
2
Votes
2
Replies
99
Views
How to Analyse Datasets from GEO