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18
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2.5k
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problem installing ENmix package
ENmix
Bioconductor
rtracklayer
written 3.2 years ago by
lea
• 0
0
votes
0
replies
98
views
I am trying to detect alternative splicing.
ASpli
16 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
798
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
238
views
Differential peaks that were not identified in diffbind were identified in diseq2
DiffBind
DESeq2
ATACSeq
19 days ago • updated 16 days ago
lonn
• 0
1
vote
2
replies
245
views
How to retrieve detailed regression results from deseq2
DESeq2
26 days ago • updated 17 days ago
Weiqian
▴ 10
1
vote
0
replies
286
views
Tutorial:
Installing/switching between versions of R/Rstudio/Bioconductor on personal machine (Linux | Ubuntu)
bioconductor
Install
17 days ago
BioinfGuru
▴ 30
0
votes
7
replies
423
views
DESeq filtering specific to contrasts
DESeq2
updated 17 days ago by
Michael Love
41k • written 11 weeks ago by
Emma
• 0
0
votes
2
replies
256
views
Odd behavior of Rsubread::featureCounts when setting `nonOverlap = 0`
featureCounts
Rsubread
5 weeks ago • updated 17 days ago
isaac.vock
• 0
0
votes
3
replies
155
views
Error retrieving ensembl gene id using biomaRt...
biomaRt
updated 17 days ago by
James W. MacDonald
65k • written 17 days ago by
bas_work
▴ 30
2
votes
5
replies
753
views
DESeq2 setting significant p-value
DESeq2
updated 17 days ago by
Michael Love
41k • written 5.0 years ago by
Merlin
▴ 10
2
votes
2
replies
192
views
OrgDb for maize
clusterProfiler
OrgDb
biomaRt
Zea_mays
updated 17 days ago by
James W. MacDonald
65k • written 18 days ago by
sansan
• 0
6
votes
10
replies
1.6k
views
Which input file is used for DGEList in EgdeR?
salmon
edgeR
tximport
nf-core
gene_counts
updated 17 days ago by
i.atanasoai
• 0 • written 15 months ago by
mohammedtoufiq91
▴ 10
0
votes
4
replies
270
views
DEG with low counts
DESeq2
updated 17 days ago by
Michael Love
41k • written 22 days ago by
Rajat
• 0
6
votes
5
replies
442
views
Estimating Cell Counts for EPIC V2 array data
FlowSorted.Blood.EPIC
minifi
written 9 weeks ago by
Kim
• 0
0
votes
3
replies
193
views
Finding DEGs by using edgeR
subsettingdata
edgeR
designmatrix
updated 17 days ago by
Gordon Smyth
50k • written 18 days ago by
prity6459
• 0
0
votes
2
replies
137
views
How to make DGEList and design matrix by edgeR package
DGEList
edgeR
17 days ago
prity6459
• 0
3
votes
1
reply
179
views
Log-cpm values from limma
limma
edgeR
RNASeq
updated 17 days ago by
Gordon Smyth
50k • written 18 days ago by
Shaimaa Gamal
• 0
0
votes
2
replies
920
views
Problem for loading Bioconductor package in R
Bioconductor
written 4.2 years ago by
araaaju
• 0
4
votes
8
replies
400
views
Memory errors using read.bismark?
dmrseq
bsseq
updated 18 days ago by
Peter Hickey
▴ 740 • written 25 days ago by
Juan Higareda
• 0
11
votes
5
replies
7.4k
views
Theoretical WGCNA Question
WGCNA
Theory
Scale-Free Topology
updated 18 days ago by
Garrett
• 0 • written 9.1 years ago by
brohawndg
▴ 150
0
votes
4
replies
204
views
FGSEA pre-ranked input in increasing order or decreasing
fgsea
18 days ago
sropri
• 0
1
vote
2
replies
220
views
significant difference of p-values with dream() after updating VariancePartition
variancePartition
18 days ago
Le
• 0
0
votes
3
replies
257
views
A ComBat-seq issue: the covariates are confounded
ComBat-seq
sva
updated 18 days ago by
W. Evan Johnson
▴ 850 • written 24 days ago by
schlumbohm
• 0
0
votes
0
replies
121
views
Warning while loading DEP package
DEP
updated 18 days ago by
shepherl
3.9k • written 18 days ago by
Namrata
• 0
0
votes
1
reply
156
views
Adding columns to DEXSeqResults object
DEXSeq
updated 18 days ago by
Alejandro Reyes
★ 1.9k • written 20 days ago by
Clyde
• 0
0
votes
1
reply
139
views
rlog transformation
DESeq2
updated 18 days ago by
Michael Love
41k • written 18 days ago by
ishij9717
• 0
0
votes
1
reply
113
views
ONT long-read RNA sequencing - data analysis options
DESeq2
LongRead
DEXSeq
IsoformSwitchAnalyzeR
RNASeq
updated 18 days ago by
Michael Love
41k • written 18 days ago by
09191919
• 0
0
votes
1
reply
135
views
covariate with negative and positive values
DESeq2
updated 18 days ago by
Michael Love
41k • written 20 days ago by
Brynn
• 0
1
vote
2
replies
158
views
Error in champ.load(): The following specified files do not exist
ChAMP
19 days ago • updated 18 days ago
Sherin
• 0
9
votes
12
replies
7.8k
views
Multi factor design edgeR/Deseq2
deseq2
edgeR
rna-seq
updated 18 days ago by
Elizabeth
• 0 • written 8.8 years ago by
gthm
▴ 30
5
votes
9
replies
930
views
Light difference when using coef vs omit a group when compare 3 groups.
limma
26 days ago • updated 18 days ago
Chris
• 0
0
votes
1
reply
101
views
Input Question for deseq.r
RSeqAn
updated 18 days ago by
ATpoint
★ 4.1k • written 19 days ago by
Nina
• 0
0
votes
1
reply
150
views
DESEQ2 output gives multiple groups when only 2 groups are present
DESeq2
updated 18 days ago by
ATpoint
★ 4.1k • written 19 days ago by
quanah.hudson
• 0
3
votes
3
replies
208
views
Reading huge bismark coverage files using bbseq::read.bismark
HDF5Array
BiocGenerics
BiocParallel
Biobase
24 days ago • updated 18 days ago
jacques.imbert
• 0
5
votes
9
replies
1.3k
views
Batch correction and repeated measures
RUVSeq
sva
limma
updated 19 days ago by
Gordon Smyth
50k • written 7 months ago by
Jonathan
▴ 10
3
votes
18
replies
2.9k
views
News:
List of Deprecated Packages for Bioc3.18
Deprecation
devel
Bioconductor
Devel
10 months ago • updated 19 days ago
shepherl
3.9k
0
votes
2
replies
921
views
Single-Cell Data Simulation from Bulk RNA-seq
SingleCell
RNASeq
RNASeqData
scRNAseq
updated 19 days ago by
wichaidi
• 0 • written 17 months ago by
irvin.ng
• 0
1
vote
7
replies
1.8k
views
Error using champ.import
ChAMP
EPICv2
updated 19 days ago by
shilpa
• 0 • written 10 months ago by
medha.suman
• 0
2
votes
5
replies
1.1k
views
DESeq2 remove batch effect
BatchEffect
RNASeqData
WGCNA
DESeq2
updated 19 days ago by
Ashley
• 0 • written 10 months ago by
zxc741xb
• 0
0
votes
0
replies
83
views
News:
Services
flowBeads
19 days ago
creativepeptides2018
• 0
0
votes
0
replies
81
views
Enzyme Engineering
BioTIP
19 days ago
bocchemistry
• 0
0
votes
0
replies
82
views
News:
TIDES USA 2024
flowBeads
19 days ago
bocsci11
• 0
0
votes
0
replies
94
views
Syntaxt Error in IsorcorrectoR package with Molecule Info File
Syntaxerror
IsoCorrectoR
20 days ago
Maliha Tabassum
• 0
0
votes
4
replies
602
views
How to correct for known and surrogate variables in DESeq2?
DESeq2
BatchEffect
sva
limma
updated 20 days ago by
Michael Love
41k • written 6 months ago by
Crystal571
• 0
0
votes
4
replies
195
views
flowStats Search Error
flowStats
updated 20 days ago by
shepherl
3.9k • written 21 days ago by
tholmes
• 0
0
votes
1
reply
139
views
SNP locus package for mouse?
SNPlocs
packFinder
updated 20 days ago by
James W. MacDonald
65k • written 23 days ago by
tian.liu0720
• 0
1
vote
2
replies
141
views
geneList error in clusterprofiler
clusterProfiler
GeneSetEnrichment
20 days ago
Ana
• 0
0
votes
1
reply
121
views
what is the sampleFiles
chipseq
updated 20 days ago by
James W. MacDonald
65k • written 20 days ago by
zhulin
• 0
0
votes
3
replies
207
views
Interaction Terms in DESeq2 - Shrinkage
DESeq2
updated 20 days ago by
Michael Love
41k • written 21 days ago by
andrebolerbarros
▴ 20
45,624 results • Page
3 of 913
Recent ...
Replies
Comment: Mac ARM64 build report for BioC 3.19 from 'kjohnson3' reporting ERROR which it
by
Hervé Pagès
16k
Indeed. Calculations involving floating point arithmetic are architecture-dependent, and testing the results should be done with `all.equal…
Comment: How to use bootRanges to bootstrap small RNA loci (nullranges package)
by
Poonam
• 0
I will follow what you suggested. I didn't use max gap anywhere. I was following statistic I and regarding the size of features, my small…
Comment: How to use bootRanges to bootstrap small RNA loci (nullranges package)
by
Michael Love
41k
Oh I see, for the second question, I don't have a great answer. I typically think of one set as the anchor, whose ascertainment is driving …
Comment: Help with running egsea()
by
James W. MacDonald
65k
Oh, right. Ideally you would use NCBI (aka Entrez gene) IDs because they are way more likely to be unique. Gene symbols are broken down int…
Comment: Help with running egsea()
by
Chris
• 0
Thanks James! I update the question. The last question mean when we use `buildIdx()`, could we use gene symbol instead of entrezID. However…
Votes
Answer: Mac ARM64 build report for BioC 3.19 from 'kjohnson3' reporting ERROR which it
Comment: Help with running egsea()
Answer: Trim/Filter out-of-bounds GRanges
Comment: Help with running egsea()
Answer: How to save the DEXSeq results
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Malcolm Cook
★ 1.6k
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