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4
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6
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469
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FilterByExpr low counts with small sample size
edgeR
4 weeks ago • updated 25 days ago
Jonathan
▴ 10
0
votes
1
reply
136
views
FDR via q-value
qvalue
updated 25 days ago by
James W. MacDonald
65k • written 28 days ago by
John
• 0
6
votes
12
replies
5.1k
views
BiocFileCache/ExperimentHub/AnnotationHub temporary ERROR
BiocFileCache
AnnotationHub
ExperimentHub
6 months ago • updated 25 days ago
shepherl
3.9k
3
votes
2
replies
229
views
Cannabis and KEGGgraph
KEGGREST
GenomicDistributionsData
KEGGgraph
KEGG
updated 26 days ago by
Guido Hooiveld
★ 4.0k • written 28 days ago by
fernanda.backsouza
▴ 10
0
votes
2
replies
237
views
RNAseq:Technical replicates from different batches
technicalReplicates
BatchEffect
limma
RNASeq
28 days ago • updated 26 days ago
catv
• 0
0
votes
0
replies
94
views
Unlocking Potential: NURS FPX Strategies and Insights
levi
NURSFPX
ragene20sttranscriptcluster.db
ssrch
27 days ago
vaxahey107
• 0
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
18
replies
2.6k
views
problem installing ENmix package
ENmix
Bioconductor
rtracklayer
written 3.2 years ago by
lea
• 0
0
votes
0
replies
105
views
I am trying to detect alternative splicing.
ASpli
27 days ago
Sebashish
• 0
3
votes
1
reply
1.5k
views
Job:
Post Doctoral position in AI (Deep learning / Machine learning) approaches for Cancer Research, MRC Cancer Unit, University of Cambridge, UK
job
Job
machine learning
deep learning
computational biology
written 6.3 years ago by
Shamith.Samarajiwa
▴ 180
0
votes
2
replies
818
views
Job:
Bioinformatics Laboratory Head in AI or machine learning (WEHI, Australia)
bioconductor
artificialintelligence
JobPosting
machinelearning
written 8 months ago by
Gordon Smyth
50k
0
votes
4
replies
263
views
Differential peaks that were not identified in diffbind were identified in diseq2
DiffBind
DESeq2
ATACSeq
4 weeks ago • updated 28 days ago
lonn
• 0
1
vote
2
replies
262
views
How to retrieve detailed regression results from deseq2
DESeq2
5 weeks ago • updated 28 days ago
Weiqian
▴ 10
1
vote
0
replies
348
views
Tutorial:
Installing/switching between versions of R/Rstudio/Bioconductor on personal machine (Linux | Ubuntu)
bioconductor
Install
28 days ago
BioinfGuru
▴ 30
0
votes
7
replies
447
views
DESeq filtering specific to contrasts
DESeq2
updated 28 days ago by
Michael Love
42k • written 3 months ago by
Emma
• 0
0
votes
2
replies
281
views
Odd behavior of Rsubread::featureCounts when setting `nonOverlap = 0`
featureCounts
Rsubread
6 weeks ago • updated 28 days ago
isaac.vock
• 0
0
votes
3
replies
173
views
Error retrieving ensembl gene id using biomaRt...
biomaRt
updated 28 days ago by
James W. MacDonald
65k • written 28 days ago by
bas_work
▴ 30
2
votes
5
replies
791
views
DESeq2 setting significant p-value
DESeq2
updated 28 days ago by
Michael Love
42k • written 5.0 years ago by
Merlin
▴ 10
2
votes
2
replies
212
views
OrgDb for maize
clusterProfiler
OrgDb
biomaRt
Zea_mays
updated 28 days ago by
James W. MacDonald
65k • written 29 days ago by
sansan
• 0
6
votes
10
replies
1.7k
views
Which input file is used for DGEList in EgdeR?
salmon
edgeR
tximport
nf-core
gene_counts
updated 28 days ago by
i.atanasoai
• 0 • written 15 months ago by
mohammedtoufiq91
▴ 10
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
6
votes
5
replies
474
views
Estimating Cell Counts for EPIC V2 array data
FlowSorted.Blood.EPIC
minifi
written 11 weeks ago by
Kim
• 0
0
votes
3
replies
210
views
Finding DEGs by using edgeR
subsettingdata
edgeR
designmatrix
updated 29 days ago by
Gordon Smyth
50k • written 29 days ago by
prity6459
• 0
0
votes
2
replies
147
views
How to make DGEList and design matrix by edgeR package
DGEList
edgeR
29 days ago
prity6459
• 0
0
votes
2
replies
929
views
Problem for loading Bioconductor package in R
Bioconductor
written 4.3 years ago by
araaaju
• 0
11
votes
5
replies
7.4k
views
Theoretical WGCNA Question
WGCNA
Theory
Scale-Free Topology
updated 29 days ago by
Garrett
• 0 • written 9.2 years ago by
brohawndg
▴ 150
0
votes
4
replies
216
views
FGSEA pre-ranked input in increasing order or decreasing
fgsea
29 days ago
sropri
• 0
1
vote
2
replies
235
views
significant difference of p-values with dream() after updating VariancePartition
variancePartition
4 weeks ago • updated 29 days ago
Le
• 0
0
votes
3
replies
281
views
A ComBat-seq issue: the covariates are confounded
ComBat-seq
sva
updated 29 days ago by
W. Evan Johnson
▴ 850 • written 5 weeks ago by
schlumbohm
• 0
0
votes
0
replies
132
views
Warning while loading DEP package
DEP
updated 29 days ago by
shepherl
3.9k • written 29 days ago by
Namrata
• 0
0
votes
1
reply
166
views
Adding columns to DEXSeqResults object
DEXSeq
updated 29 days ago by
Alejandro Reyes
★ 1.9k • written 4 weeks ago by
Clyde
• 0
0
votes
1
reply
157
views
rlog transformation
DESeq2
updated 29 days ago by
Michael Love
42k • written 4 weeks ago by
ishij9717
• 0
0
votes
1
reply
125
views
ONT long-read RNA sequencing - data analysis options
DESeq2
LongRead
DEXSeq
IsoformSwitchAnalyzeR
RNASeq
updated 29 days ago by
Michael Love
42k • written 4 weeks ago by
09191919
• 0
0
votes
1
reply
149
views
covariate with negative and positive values
DESeq2
updated 29 days ago by
Michael Love
42k • written 4 weeks ago by
Brynn
• 0
1
vote
2
replies
178
views
Error in champ.load(): The following specified files do not exist
ChAMP
4 weeks ago • updated 29 days ago
Sherin
• 0
9
votes
12
replies
7.9k
views
Multi factor design edgeR/Deseq2
deseq2
edgeR
rna-seq
updated 29 days ago by
Elizabeth
• 0 • written 8.9 years ago by
gthm
▴ 30
5
votes
9
replies
974
views
Light difference when using coef vs omit a group when compare 3 groups.
limma
5 weeks ago • updated 29 days ago
Chris
▴ 10
0
votes
1
reply
111
views
Input Question for deseq.r
RSeqAn
updated 29 days ago by
ATpoint
★ 4.1k • written 4 weeks ago by
Nina
• 0
0
votes
1
reply
166
views
DESEQ2 output gives multiple groups when only 2 groups are present
DESeq2
updated 29 days ago by
ATpoint
★ 4.1k • written 4 weeks ago by
quanah.hudson
• 0
3
votes
3
replies
244
views
Reading huge bismark coverage files using bbseq::read.bismark
HDF5Array
BiocGenerics
BiocParallel
Biobase
5 weeks ago • updated 4 weeks ago
jacques.imbert
• 0
5
votes
9
replies
1.3k
views
Batch correction and repeated measures
RUVSeq
sva
limma
updated 4 weeks ago by
Gordon Smyth
50k • written 7 months ago by
Jonathan
▴ 10
3
votes
18
replies
3.0k
views
News:
List of Deprecated Packages for Bioc3.18
Deprecation
devel
Bioconductor
Devel
10 months ago • updated 4 weeks ago
shepherl
3.9k
0
votes
2
replies
953
views
Single-Cell Data Simulation from Bulk RNA-seq
SingleCell
RNASeq
RNASeqData
scRNAseq
updated 4 weeks ago by
wichaidi
• 0 • written 18 months ago by
irvin.ng
• 0
1
vote
7
replies
1.9k
views
Error using champ.import
ChAMP
EPICv2
updated 4 weeks ago by
shilpa
• 0 • written 10 months ago by
medha.suman
• 0
2
votes
5
replies
1.2k
views
DESeq2 remove batch effect
BatchEffect
RNASeqData
WGCNA
DESeq2
updated 4 weeks ago by
Ashley
• 0 • written 11 months ago by
zxc741xb
• 0
0
votes
0
replies
95
views
News:
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flowBeads
4 weeks ago
creativepeptides2018
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0
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91
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Enzyme Engineering
BioTIP
4 weeks ago
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0
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0
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96
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News:
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flowBeads
4 weeks ago
bocsci11
• 0
0
votes
0
replies
105
views
Syntaxt Error in IsorcorrectoR package with Molecule Info File
Syntaxerror
IsoCorrectoR
4 weeks ago
Maliha Tabassum
• 0
0
votes
4
replies
629
views
How to correct for known and surrogate variables in DESeq2?
DESeq2
BatchEffect
sva
limma
updated 4 weeks ago by
Michael Love
42k • written 6 months ago by
Crystal571
• 0
45,666 results • Page
4 of 914
Recent ...
Replies
Comment: Numerical differences in DESeq2 output depending on different design matrix cons
by
JKim
• 0
The 1st model has an interaction term, but the 2nd model doesn't have the interaction term. That makes the difference.
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…
Comment: STRINGdb : error with string_db$plot_network()
by
damian.szk
▴ 80
ok. Forcing non-secure protocol should not be needed anymore, due to changes in the underlying library. However, I will look at why "HTTP" …
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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