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News:
Nominations for Bioconductor Awards 2024!
Recognition
Awards
Bioconductor
Bioc204
6 weeks ago • updated 1 day ago
shepherl
3.9k
0
votes
3
replies
207
views
Interaction Terms in DESeq2 - Shrinkage
DESeq2
updated 21 days ago by
Michael Love
42k • written 22 days ago by
andrebolerbarros
▴ 20
0
votes
4
replies
206
views
FGSEA pre-ranked input in increasing order or decreasing
fgsea
19 days ago
sropri
• 0
2
votes
2
replies
203
views
Perform gene set enrichment analysis using fgsea on two conditions that don't have differential express genes
fgsea
8 days ago
Chris
• 0
1
vote
2
replies
199
views
Design Matrix within group comparison more than two groups
DESeq2
25 days ago • updated 24 days ago
hemantcnaik
• 0
2
votes
2
replies
198
views
How many of my genes from my gene list are in each KEGG pathway?
Pathways
clusterProfiler
gseKEGG
KEGG
25 days ago
julia_mcdonough
• 0
0
votes
4
replies
195
views
flowStats Search Error
flowStats
updated 21 days ago by
shepherl
3.9k • written 22 days ago by
tholmes
• 0
0
votes
3
replies
193
views
Finding DEGs by using edgeR
subsettingdata
edgeR
designmatrix
updated 18 days ago by
Gordon Smyth
50k • written 19 days ago by
prity6459
• 0
2
votes
2
replies
193
views
OrgDb for maize
clusterProfiler
OrgDb
biomaRt
Zea_mays
updated 18 days ago by
James W. MacDonald
65k • written 19 days ago by
sansan
• 0
1
vote
2
replies
191
views
Improving the design matrices vignette in RNAseq123
RNAseq123
15 days ago • updated 1 day ago
Lluís Revilla Sancho
▴ 730
1
vote
1
reply
188
views
Differentially expressed genes in monocle pseudotime
monocle
updated 21 days ago by
Gordon Smyth
50k • written 23 days ago by
kthapa
• 0
2
votes
3
replies
182
views
Too many significant genes when integrating gtex and tcga
RNA-seq
DESeq2
updated 2 days ago by
ATpoint
★ 4.1k • written 4 days ago by
Reza
• 0
0
votes
1
reply
182
views
How can I create a GO plot with ggpubr and clusterProfiler libraries (begginer)
clusterProfiler
ggpubr
updated 29 days ago by
James W. MacDonald
65k • written 4 weeks ago by
BCS12
• 0
1
vote
1
reply
179
views
Citation for edgeR user guide
edgeR
updated 14 days ago by
Gordon Smyth
50k • written 14 days ago by
k___
▴ 30
3
votes
1
reply
179
views
Log-cpm values from limma
limma
edgeR
RNASeq
updated 18 days ago by
Gordon Smyth
50k • written 19 days ago by
Shaimaa Gamal
• 0
0
votes
1
reply
178
views
DESeq2 gives an error and R crashes
DESeq2
27 days ago • updated 26 days ago
Shefali
• 0
2
votes
2
replies
175
views
ComplexHeatmap: change the names of a HeatmapAnnotation object
ComplexHeatmap
25 days ago • updated 22 days ago
daniel.carbajo
• 0
0
votes
3
replies
172
views
Different number of exons in reference genome affects DEXSeq analysis
DEXSeq
updated 7 days ago by
Alejandro Reyes
★ 1.9k • written 19 days ago by
Alessia
• 0
2
votes
2
replies
172
views
[DiffBind] Obtaining normalization factors
DiffBind
25 days ago • updated 21 days ago
Henry
▴ 10
0
votes
2
replies
170
views
limma-voom: Calculate the log-fold change in gene expression within a sample
limma
RNASeq
voom
written 15 days ago by
taur.vil
• 0
3
votes
4
replies
169
views
Method to find pathways different between 2 groups
fgsea
GSVA
CAMERA
updated 2 hours ago by
Gordon Smyth
50k • written 2 days ago by
Chris
• 0
0
votes
1
reply
167
views
IgG control in RIP-seq with Deseq2
DESeq2
RIP-seq
updated 28 days ago by
Michael Love
42k • written 28 days ago by
Adelaide
• 0
2
votes
3
replies
167
views
package goseq seems to be not available on the latest version of R
goseq
updated 1 day ago by
Gordon Smyth
50k • written 4 days ago by
Patrycja
▴ 20
1
vote
2
replies
161
views
Getting Error in hclust(d, method = method): NA/NaN/Inf in foreign function call when trying to subset pheatmap
DESeq2
6 days ago • updated 41 minutes ago
angelathuynh5
• 0
0
votes
1
reply
162
views
compareCluster dotplot: how to modify the genesets order
DOSE
enrichplot
clusterProfiler
updated 23 days ago by
Guido Hooiveld
★ 3.9k • written 27 days ago by
Lucie
• 0
0
votes
3
replies
162
views
Store output of matchPWM()
biostrings
Biostrings
updated 6 days ago by
James W. MacDonald
65k • written 6 days ago by
mat149
▴ 70
1
vote
2
replies
161
views
Reproducibility issue with scran together with lapply and BiocParallel
scran
BiocParallel
bluster
13 days ago • updated 12 days ago
ATpoint
★ 4.1k
1
vote
2
replies
160
views
Error in champ.load(): The following specified files do not exist
ChAMP
20 days ago • updated 19 days ago
Sherin
• 0
0
votes
1
reply
158
views
Adding columns to DEXSeqResults object
DEXSeq
updated 19 days ago by
Alejandro Reyes
★ 1.9k • written 21 days ago by
Clyde
• 0
0
votes
3
replies
156
views
Error retrieving ensembl gene id using biomaRt...
biomaRt
updated 18 days ago by
James W. MacDonald
65k • written 18 days ago by
bas_work
▴ 30
0
votes
1
reply
155
views
DESEQ2 IHW and Apelgm method for Shrinkage (adding s values to FDR)
DESeq2
RNAseq
updated 13 days ago by
Michael Love
42k • written 13 days ago by
kcarey
• 0
0
votes
1
reply
152
views
BAM write error in HTSeqGenie
HTSeqGenie
BAM
updated 28 days ago by
James W. MacDonald
65k • written 28 days ago by
zh9118
• 0
0
votes
3
replies
151
views
Differences in differential analysis methods for RNA-Seq
DESeq2
StatisticalMethod
Proteomics
DifferentialExpression
RNASeq
updated 5 days ago by
ATpoint
★ 4.1k • written 6 days ago by
james.zhang20
• 0
3
votes
4
replies
151
views
Help with running egsea()
EGSEA
1 day ago • updated 4 hours ago
Chris
• 0
0
votes
1
reply
150
views
DESEQ2 output gives multiple groups when only 2 groups are present
DESeq2
updated 19 days ago by
ATpoint
★ 4.1k • written 20 days ago by
quanah.hudson
• 0
0
votes
0
replies
149
views
Job:
PhD-position in bioinformatics / computational biology
Mergeomics
Epigenome
Evolution
NGS
Aging
29 days ago
arne.sahm
• 0
0
votes
2
replies
149
views
Deseq2 and Normalization of RNA sequencing data
DESeq2
6 days ago • updated 5 days ago
kcarey
• 0
0
votes
1
reply
145
views
The issue with SGSeq_analyzeFeatures() returns errors on BAM files
SGSeq
updated 21 days ago by
kamryncole1963
• 0 • written 26 days ago by
Sara
• 0
0
votes
1
reply
143
views
SNP locus package for mouse?
SNPlocs
packFinder
updated 21 days ago by
James W. MacDonald
65k • written 24 days ago by
tian.liu0720
• 0
1
vote
2
replies
142
views
geneList error in clusterprofiler
clusterProfiler
GeneSetEnrichment
21 days ago
Ana
• 0
0
votes
1
reply
141
views
Can you find the correct transcript in scRNA seq data
scRNAseq
RNAseq
updated 27 days ago by
ATpoint
★ 4.1k • written 29 days ago by
Merav
• 0
2
votes
2
replies
141
views
fgsea significant result
fgsea
3 days ago • updated 2 days ago
Chris
• 0
0
votes
1
reply
140
views
ATACseq merge peaks
DiffBind
updated 11 days ago by
ATpoint
★ 4.1k • written 13 days ago by
Shloka
• 0
0
votes
2
replies
139
views
More regions in union when increasing DBA$config$mergeOverlap
DiffBind
6 days ago • updated 5 days ago
Ian D.
▴ 70
0
votes
1
reply
139
views
rlog transformation
DESeq2
updated 19 days ago by
Michael Love
42k • written 19 days ago by
ishij9717
• 0
0
votes
1
reply
137
views
Bioinformatics student
Des
DESeq2
updated 25 days ago by
hemantcnaik
• 0 • written 25 days ago by
Sahar
• 0
0
votes
2
replies
137
views
How to make DGEList and design matrix by edgeR package
DGEList
edgeR
18 days ago
prity6459
• 0
0
votes
1
reply
135
views
covariate with negative and positive values
DESeq2
updated 19 days ago by
Michael Love
42k • written 21 days ago by
Brynn
• 0
0
votes
0
replies
135
views
LearnTaxa with custom Silva
DECIPHER
LearnTaxa
27 days ago
Eryn
• 0
1
vote
1
reply
134
views
Dominance Index for Shotgun Metagenomics Data
microbiome
updated 11 days ago by
Leo Lahti
▴ 40 • written 11 days ago by
Dario Strbenac
★ 1.5k
201 results • Page
3 of 5
Recent ...
Replies
Comment: Getting Error in hclust(d, method = method): NA/NaN/Inf in foreign function call
by
angelathuynh5
• 0
Thank you for your response. To clarify, the process of making a heatmap performs rowscaling so it takes the value - (mean/std). And to res…
Comment: Limma without eBayes, is it indistunguishable from Ordinary Least Square?
by
Gordon Smyth
50k
The formula given in the original question is correct and yours is not. Your formula isn't even constrained to be between 0 and 1. Here is …
Comment: Method to find pathways different between 2 groups
by
Gordon Smyth
50k
sigPathway is another method that does not account for inter-gene correlation and which gives inflated significance, as we showed in our 20…
Answer: error in limma , contrast.matrix Number of rows of contrast matrix must match nu
by
James W. MacDonald
65k
I doubt you have that many contrasts. I think that is probably the number of rows. What does `dim(fit)` return (and `head(fit$coef)`)?
Answer: Extremely small p-values using Limma for proteomic data
by
James W. MacDonald
65k
If you fit a cell means model (without an intercept), you will have to construct contrasts using `makeContrasts` and fit them using `contra…
Votes
Answer: Getting Error in hclust(d, method = method): NA/NaN/Inf in foreign function call
Answer: error in limma , contrast.matrix Number of rows of contrast matrix must match nu
Answer: Extremely small p-values using Limma for proteomic data
Answer: How to save the DEXSeq results
Answer: minfi support of illumina Infinium methylationEPIC v2.0
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Gyan Prakash Mishra
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50k
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