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0
replies
91
views
Exon-exon Junction Analysis for Variable-length Exons
Rsubread
17 days ago
Dario Strbenac
★ 1.5k
1
vote
3
replies
226
views
Different Shrunk Log2FC according with reference
DESeq2
updated 17 days ago by
Michael Love
42k • written 17 days ago by
andrebolerbarros
▴ 20
1
vote
3
replies
875
views
How to tell and visualize up/down regulation of pathways from clusterprofiler gsea output
clusterProfiler
RNASeq
updated 17 days ago by
Guangchuang Yu
★ 1.2k • written 14 months ago by
ruiqi.li
▴ 10
1
vote
4
replies
215
views
minfi::read.metharray.exp
minfiData
minfi
updated 17 days ago by
Basti
▴ 780 • written 19 days ago by
clacarion
• 0
3
votes
1
reply
319
views
Use of negative binomial model for exponential decay rate estimation using DESeq (or similar)
DESeq2
updated 18 days ago by
Michael Love
42k • written 18 days ago by
i.sudbery
▴ 40
1
vote
1
reply
184
views
Citation for edgeR user guide
edgeR
updated 18 days ago by
Gordon Smyth
50k • written 18 days ago by
k___
▴ 30
0
votes
7
replies
727
views
News:
List of Deprecated Packages for Bioc3.19
Release
Devel
ExperimentData
Software
10 weeks ago • updated 18 days ago
shepherl
3.9k
1
vote
1
reply
122
views
Cannabis OrgDb
KEGGgraph
org.Cs.eg.db
clusterProfiler
KEGG
AnnotationHubSoftware
updated 18 days ago by
James W. MacDonald
65k • written 18 days ago by
fernanda.backsouza
▴ 10
0
votes
0
replies
77
views
News:
Interested in the analysis of Spatial Omics data?
tidySpatialExperiment
SpatialExperiment
MoleculeExperiment
18 days ago
info
▴ 10
3
votes
3
replies
235
views
DESeq2 - dispersion estimation when there is none
DESeq2
updated 18 days ago by
Michael Love
42k • written 19 days ago by
WardDeb
• 0
0
votes
7
replies
333
views
Methylation Analysis experiment design using Limma
DNAMethylation
limma
methylationArrayAnalysis
24 days ago • updated 18 days ago
hortense96
• 0
5
votes
8
replies
8.8k
views
Limma design with continuous and categorical covariates
limma
batch effect
covariates
microarray
updated 18 days ago by
hortense96
• 0 • written 7.7 years ago by
dmcleanuk
▴ 30
1
vote
2
replies
1.0k
views
DMR.Plot shows error "Error in simpleLoess(y, x, w, span, degree = degree, parametric = FALSE, : NA/NaN/Inf in foreign function call (arg 1)"
DMRcate
Gviz
updated 19 days ago by
Tim Peters
▴ 180 • written 14 months ago by
jose.ramirez1
▴ 10
1
vote
4
replies
253
views
Error EPICv2 ChAMP
ChAMPdata
IlluminaHumanMethylationEPICv2anno.20a1.hg38
ChAMP
updated 19 days ago by
James W. MacDonald
65k • written 23 days ago by
Mirella Aurora
• 0
4
votes
6
replies
449
views
FilterByExpr low counts with small sample size
edgeR
24 days ago • updated 19 days ago
Jonathan
▴ 10
0
votes
1
reply
131
views
FDR via q-value
qvalue
updated 19 days ago by
James W. MacDonald
65k • written 22 days ago by
John
• 0
6
votes
12
replies
5.0k
views
BiocFileCache/ExperimentHub/AnnotationHub temporary ERROR
BiocFileCache
AnnotationHub
ExperimentHub
6 months ago • updated 19 days ago
shepherl
3.9k
3
votes
2
replies
220
views
Cannabis and KEGGgraph
KEGGREST
GenomicDistributionsData
KEGGgraph
KEGG
updated 19 days ago by
Guido Hooiveld
★ 3.9k • written 22 days ago by
fernanda.backsouza
▴ 10
0
votes
2
replies
223
views
RNAseq:Technical replicates from different batches
technicalReplicates
BatchEffect
limma
RNASeq
22 days ago • updated 19 days ago
catv
• 0
0
votes
3
replies
1.2k
views
News:
European Bioconductor Conference 2023 planning
Europe
Conference
EuroBioC
Events
News
updated 20 days ago by
lauryfriese932
• 0 • written 18 months ago by
Maria Doyle
▴ 70
0
votes
0
replies
86
views
Unlocking Potential: NURS FPX Strategies and Insights
levi
NURSFPX
ragene20sttranscriptcluster.db
ssrch
20 days ago
vaxahey107
• 0
3
votes
3
replies
356
views
permutation test in edgeR
rna-seq
edgeR
updated 20 days ago by
Gordon Smyth
50k • written 4 weeks ago by
Netanel
• 0
0
votes
18
replies
2.5k
views
problem installing ENmix package
ENmix
Bioconductor
rtracklayer
written 3.2 years ago by
lea
• 0
0
votes
0
replies
102
views
I am trying to detect alternative splicing.
ASpli
21 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
805
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
247
views
Differential peaks that were not identified in diffbind were identified in diseq2
DiffBind
DESeq2
ATACSeq
24 days ago • updated 21 days ago
lonn
• 0
1
vote
2
replies
250
views
How to retrieve detailed regression results from deseq2
DESeq2
4 weeks ago • updated 22 days ago
Weiqian
▴ 10
1
vote
0
replies
311
views
Tutorial:
Installing/switching between versions of R/Rstudio/Bioconductor on personal machine (Linux | Ubuntu)
bioconductor
Install
22 days ago
BioinfGuru
▴ 30
0
votes
7
replies
435
views
DESeq filtering specific to contrasts
DESeq2
updated 22 days ago by
Michael Love
42k • written 12 weeks ago by
Emma
• 0
0
votes
2
replies
267
views
Odd behavior of Rsubread::featureCounts when setting `nonOverlap = 0`
featureCounts
Rsubread
5 weeks ago • updated 22 days ago
isaac.vock
• 0
0
votes
3
replies
164
views
Error retrieving ensembl gene id using biomaRt...
biomaRt
updated 22 days ago by
James W. MacDonald
65k • written 22 days ago by
bas_work
▴ 30
2
votes
5
replies
773
views
DESeq2 setting significant p-value
DESeq2
updated 22 days ago by
Michael Love
42k • written 5.0 years ago by
Merlin
▴ 10
2
votes
2
replies
199
views
OrgDb for maize
clusterProfiler
OrgDb
biomaRt
Zea_mays
updated 22 days ago by
James W. MacDonald
65k • written 23 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 22 days ago by
i.atanasoai
• 0 • written 15 months ago by
mohammedtoufiq91
▴ 10
0
votes
4
replies
280
views
DEG with low counts
DESeq2
updated 22 days ago by
Michael Love
42k • written 27 days ago by
Rajat
• 0
6
votes
5
replies
458
views
Estimating Cell Counts for EPIC V2 array data
FlowSorted.Blood.EPIC
minifi
written 10 weeks ago by
Kim
• 0
0
votes
3
replies
196
views
Finding DEGs by using edgeR
subsettingdata
edgeR
designmatrix
updated 22 days ago by
Gordon Smyth
50k • written 23 days ago by
prity6459
• 0
0
votes
2
replies
142
views
How to make DGEList and design matrix by edgeR package
DGEList
edgeR
22 days ago
prity6459
• 0
0
votes
2
replies
923
views
Problem for loading Bioconductor package in R
Bioconductor
written 4.2 years ago by
araaaju
• 0
11
votes
5
replies
7.4k
views
Theoretical WGCNA Question
WGCNA
Theory
Scale-Free Topology
updated 23 days ago by
Garrett
• 0 • written 9.1 years ago by
brohawndg
▴ 150
0
votes
4
replies
210
views
FGSEA pre-ranked input in increasing order or decreasing
fgsea
23 days ago
sropri
• 0
1
vote
2
replies
227
views
significant difference of p-values with dream() after updating VariancePartition
variancePartition
23 days ago
Le
• 0
0
votes
3
replies
269
views
A ComBat-seq issue: the covariates are confounded
ComBat-seq
sva
updated 23 days ago by
W. Evan Johnson
▴ 850 • written 29 days ago by
schlumbohm
• 0
0
votes
0
replies
126
views
Warning while loading DEP package
DEP
updated 23 days ago by
shepherl
3.9k • written 23 days ago by
Namrata
• 0
0
votes
1
reply
162
views
Adding columns to DEXSeqResults object
DEXSeq
updated 23 days ago by
Alejandro Reyes
★ 1.9k • written 25 days ago by
Clyde
• 0
0
votes
1
reply
144
views
rlog transformation
DESeq2
updated 23 days ago by
Michael Love
42k • written 23 days ago by
ishij9717
• 0
0
votes
1
reply
118
views
ONT long-read RNA sequencing - data analysis options
DESeq2
LongRead
DEXSeq
IsoformSwitchAnalyzeR
RNASeq
updated 23 days ago by
Michael Love
42k • written 23 days ago by
09191919
• 0
0
votes
1
reply
138
views
covariate with negative and positive values
DESeq2
updated 23 days ago by
Michael Love
42k • written 25 days ago by
Brynn
• 0
1
vote
2
replies
167
views
Error in champ.load(): The following specified files do not exist
ChAMP
24 days ago • updated 23 days ago
Sherin
• 0
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Comment: More regions in union when increasing DBA$config$mergeOverlap
by
Ziliang
• 0
I am so confused and frustrated learning to use this software. Isn't how you merge the peaksets one of the most important steps for the com…
Answer: SingleR Label.Ont
by
Denis
• 0
[Jackpot City Casino][1] is the perfect option when looking for an online casino in Canada for an exciting vacation and huge winnings that …
Comment: deseq2 results
by
sajadahmad41454
• 0
thank you so much and sorry for bothering you again and again, it is urgent because it is my project deadline. i have removed that sample a…
Comment: deseq2 results
by
swbarnes2
★ 1.4k
Ask the people who made the libraires if there was anything unusual in the QC of the outlier sample. Try to figure out what biologically …
Comment: Can't post a question containing code?
by
NATASHA
• 0
did you find a solution? I´m having the same problem
Votes
A: AIC-like measure for DESeq2
Comment: Extremely small p-values using Limma for proteomic data
Comment: Log-cpm values from limma
Comment: Log-cpm values from limma
Comment: deseq2 results
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