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0
replies
82
views
[ChIPseeker] Unable to perform gene ontology analysis
ChIPseeker
4 weeks ago
Henry
▴ 10
0
votes
3
replies
230
views
Interaction Terms in DESeq2 - Shrinkage
DESeq2
updated 4 weeks ago by
Michael Love
42k • written 4 weeks ago by
andrebolerbarros
▴ 20
2
votes
3
replies
345
views
ComplexHeatmap: add pch to rowAnnotation when the input is a data frame with variable number of continuous columns
ComplexHeatmap
4 weeks ago
daniel.carbajo
• 0
0
votes
4
replies
292
views
DEG with low counts
DESeq2
updated 29 days ago by
Michael Love
42k • written 4 weeks ago by
Rajat
• 0
1
vote
2
replies
711
views
GSVA error
GSVA
4 weeks ago
Alex
• 0
0
votes
1
reply
147
views
Deseq2 Rlog transformation
DESeq2
updated 4 weeks ago by
ATpoint
★ 4.1k • written 4 weeks ago by
Sahar
• 0
1
vote
1
reply
208
views
Differentially expressed genes in monocle pseudotime
monocle
updated 4 weeks ago by
Gordon Smyth
50k • written 4 weeks ago by
kthapa
• 0
0
votes
1
reply
152
views
SNP locus package for mouse?
SNPlocs
packFinder
updated 4 weeks ago by
James W. MacDonald
65k • written 5 weeks ago by
tian.liu0720
• 0
2
votes
2
replies
191
views
[DiffBind] Obtaining normalization factors
DiffBind
5 weeks ago • updated 4 weeks ago
Henry
▴ 10
1
vote
2
replies
211
views
Design Matrix within group comparison more than two groups
DESeq2
5 weeks ago
hemantcnaik
• 0
0
votes
1
reply
151
views
Bioinformatics student
Des
DESeq2
updated 5 weeks ago by
hemantcnaik
• 0 • written 5 weeks ago by
Sahar
• 0
2
votes
2
replies
214
views
How many of my genes from my gene list are in each KEGG pathway?
Pathways
clusterProfiler
gseKEGG
KEGG
5 weeks ago
julia_mcdonough
• 0
0
votes
0
replies
102
views
News:
Important Release 3.18 Freeze Announcment
Release
release
Bioconductor
Bioconducto
5 weeks ago
shepherl
3.9k
3
votes
3
replies
246
views
Reading huge bismark coverage files using bbseq::read.bismark
HDF5Array
BiocGenerics
BiocParallel
Biobase
5 weeks ago • updated 4 weeks ago
jacques.imbert
• 0
2
votes
2
replies
192
views
ComplexHeatmap: change the names of a HeatmapAnnotation object
ComplexHeatmap
5 weeks ago • updated 4 weeks ago
daniel.carbajo
• 0
0
votes
3
replies
286
views
A ComBat-seq issue: the covariates are confounded
ComBat-seq
sva
updated 4 weeks ago by
W. Evan Johnson
▴ 850 • written 5 weeks ago by
schlumbohm
• 0
0
votes
0
replies
104
views
Cannot use `readVcf()` on a file created with `writeVcf()`
VariantAnnotation
5 weeks ago
Stevie Pederson
• 0
2
votes
2
replies
417
views
[Diffbind] Blacklist error: Error: Invalid Normalization and Unable to apply Blacklist/Greylist
DiffBind
Normalization
5 weeks ago
Henry
▴ 10
0
votes
0
replies
117
views
News:
Course Manipulation of NGS Data for Genomic and Population Genetics Analyses
sequencing
Sequencing
SequencingData
5 weeks ago
communication
• 0
4
votes
9
replies
491
views
Memory errors using read.bismark?
dmrseq
bsseq
5 weeks ago • updated 11 days ago
Juan Higareda
• 0
3
votes
6
replies
306
views
Surrogate variable analysis for paired RNA seq experiment
RUVSeq
sva
5 weeks ago
nhaus
▴ 30
0
votes
1
reply
165
views
The issue with SGSeq_analyzeFeatures() returns errors on BAM files
SGSeq
updated 4 weeks ago by
kamryncole1963
• 0 • written 5 weeks ago by
Sara
• 0
0
votes
1
reply
196
views
DESeq2 gives an error and R crashes
DESeq2
5 weeks ago
Shefali
• 0
1
vote
2
replies
264
views
How to retrieve detailed regression results from deseq2
DESeq2
5 weeks ago • updated 29 days ago
Weiqian
▴ 10
5
votes
9
replies
975
views
Light difference when using coef vs omit a group when compare 3 groups.
limma
5 weeks ago • updated 4 weeks ago
Chris
▴ 10
0
votes
0
replies
152
views
LearnTaxa with custom Silva
DECIPHER
LearnTaxa
5 weeks ago
Eryn
• 0
0
votes
0
replies
96
views
queryDGIdb lexical error for some genes
lexicalerror
rDGIdb
DGIdb
json
5 weeks ago
Dennis
• 0
0
votes
1
reply
199
views
compareCluster dotplot: how to modify the genesets order
DOSE
enrichplot
clusterProfiler
updated 4 weeks ago by
Guido Hooiveld
★ 4.0k • written 5 weeks ago by
Lucie
• 0
0
votes
4
replies
241
views
Storing directories inside an ExperimentHub package?
ExperimentHub
5 weeks ago
Tim Barry
• 0
8
votes
23
replies
1.0k
views
Convert Seurat Object to Summarised Experiment or ExpressionSet
SummarizedExperiment
ExpressionSet
updated 5 weeks ago by
Robert Castelo
★ 3.3k • written 5 weeks ago by
Bine
▴ 40
1
vote
3
replies
369
views
Why is my gene not significantly differentially expressed?
limmaGUI
edgeR
limma
updated 4 weeks ago by
Gordon Smyth
50k • written 5 weeks ago by
Simran
• 0
0
votes
1
reply
162
views
BAM write error in HTSeqGenie
HTSeqGenie
BAM
updated 5 weeks ago by
James W. MacDonald
65k • written 5 weeks ago by
zh9118
• 0
0
votes
1
reply
187
views
IgG control in RIP-seq with Deseq2
DESeq2
RIP-seq
updated 5 weeks ago by
Michael Love
42k • written 5 weeks ago by
Adelaide
• 0
5
votes
6
replies
458
views
Not fully paired differential gene expression analysis
edgeR
DifferentialExpression
updated 5 weeks ago by
ATpoint
★ 4.1k • written 5 weeks ago by
nhaus
▴ 30
0
votes
0
replies
129
views
ggtree tip label position (depth)
ggtree
5 weeks ago
Roope
• 0
1
vote
6
replies
522
views
GSVA on separate healthy and disease datasets
GSVA
updated 5 weeks ago by
James W. MacDonald
65k • written 5 weeks ago by
Lucy
▴ 60
2
votes
6
replies
461
views
How to make boxplot with pairwise and overall p value from Limma
t.test
boxplot
limma
anova
5 weeks ago
Chris
▴ 10
0
votes
1
reply
154
views
Can you find the correct transcript in scRNA seq data
scRNAseq
RNAseq
updated 5 weeks ago by
ATpoint
★ 4.1k • written 5 weeks ago by
Merav
• 0
0
votes
0
replies
175
views
Job:
PhD-position in bioinformatics / computational biology
Mergeomics
Epigenome
Evolution
NGS
Aging
5 weeks ago
arne.sahm
• 0
0
votes
0
replies
114
views
News:
Call for proposals: European CarpentryConnect - 12-14 November 2024, at EMBL Heidelberg
carpentry
conference
5 weeks ago
Wolfgang Huber
★ 13k
3
votes
3
replies
368
views
permutation test in edgeR
rna-seq
edgeR
updated 27 days ago by
Gordon Smyth
50k • written 5 weeks ago by
Netanel
• 0
0
votes
1
reply
189
views
How can I create a GO plot with ggpubr and clusterProfiler libraries (begginer)
clusterProfiler
ggpubr
updated 5 weeks ago by
James W. MacDonald
65k • written 5 weeks ago by
BCS12
• 0
0
votes
1
reply
186
views
Limma design matrix only showing 3/4 treatments?
limma
designmatrix
updated 6 weeks ago by
Gordon Smyth
50k • written 6 weeks ago by
avery
• 0
0
votes
4
replies
331
views
Help with design.matrix
limma
6 weeks ago
andrea.rodriguez-martinez13
• 0
1
vote
3
replies
280
views
Lib sizes in the DGE object are different from original lib sizes
edgeR
DifferentialExpression
updated 6 weeks ago by
James W. MacDonald
65k • written 6 weeks ago by
Shaimaa Gamal
• 0
0
votes
0
replies
163
views
Why output of GSEA is not the same but inversed, when you have the same but inversed input data?
clusterProfiler
gseKEGG
6 weeks ago
andromeda
• 0
0
votes
2
replies
183
views
What to the log 2 fold changes mean using LRT on time course in DESeq2
DESeq2
timecourse
DifferentialExpression
updated 6 weeks ago by
James W. MacDonald
65k • written 6 weeks ago by
joshua.mannheimer
• 0
0
votes
2
replies
245
views
Interaction term vs grouping variable design considerations
DESeq2
DifferentialExpression
updated 5 weeks ago by
Michael Love
42k • written 6 weeks ago by
nhaus
▴ 30
2
votes
2
replies
219
views
Bluster and Varieties of Louvain Clulstering
bluster
updated 6 weeks ago by
ATpoint
★ 4.1k • written 6 weeks ago by
Dario Strbenac
★ 1.5k
0
votes
1
reply
144
views
Granges regionCounts not returning the expected number of entries
methylKit
6 weeks ago
Modoc Kesner
▴ 10
45,668 results • Page
4 of 914
Recent ...
Replies
Answer: Numerical differences in DESeq2 output depending on different design matrix cons
by
Michael Love
42k
Yes there can be small numerical differences in the estimated quantities because of how the algorithms decide to stop iterating.
Answer: DESeq2- Mysterious interaction suppresses DEGs
by
Michael Love
42k
Removing samples from one group nevertheless changes the variance estimation (dispersion) for all comparisons. So you could have pushed one…
Comment: Ensembl plants at annotationHub?
by
Daniele
• 0
Hi, I'm using Ensembl Plants release 59 with the IWGSC RefSeq v1.1 gene annotation. Thanks a lot for replying so quickly!
Comment: Numerical differences in DESeq2 output depending on different design matrix cons
by
swbarnes2
★ 1.4k
If you restrict yourself to, say, genes with a baseMean > 50, are the numerical differences between the two designs significant?
Comment: DESeq2- Mysterious interaction suppresses DEGs
by
shaunpeterson
• 0
The images I tried to attach didn't attach. Here is the PCA (MDS) of all the samples, with the Cortex outlier highlighed. ![enter image de…
Votes
Answer: Error while installing BiocManager::install("org.Vdahliae.eg.db")
Comment: How can I create a eigencorplot of pca created from deseq2 object with PCAtools
Answer: Importing a GraphNEL into Cytoscape with RCy3 with error: "Error in cyrestPUT(pa
Answer: Importing a GraphNEL into Cytoscape with RCy3 with error: "Error in cyrestPUT(pa
Rsubread counting peaks ATACseq
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