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News:
List of Deprecated Packages for Bioc3.18
Deprecation
devel
Bioconductor
Devel
10 months ago • updated 6 days ago
shepherl
3.8k
4
votes
8
replies
332
views
Memory errors using read.bismark?
dmrseq
bsseq
updated 5 days ago by
Peter Hickey
▴ 740 • written 12 days ago by
Juan Higareda
• 0
3
votes
3
replies
164
views
Reading huge bismark coverage files using bbseq::read.bismark
HDF5Array
BiocGenerics
BiocParallel
Biobase
11 days ago • updated 5 days ago
jacques.imbert
• 0
1
vote
2
replies
215
views
How to retrieve detailed regression results from deseq2
DESeq2
13 days ago • updated 4 days ago
Weiqian
▴ 10
0
votes
4
replies
227
views
DEG with low counts
DESeq2
updated 4 days ago by
Michael Love
41k • written 9 days ago by
Rajat
• 0
3
votes
3
replies
280
views
permutation test in edgeR
rna-seq
edgeR
updated 3 days ago by
Gordon Smyth
50k • written 16 days ago by
Netanel
• 0
0
votes
3
replies
219
views
A ComBat-seq issue: the covariates are confounded
ComBat-seq
sva
updated 5 days ago by
W. Evan Johnson
▴ 850 • written 11 days ago by
schlumbohm
• 0
5
votes
9
replies
844
views
Light difference when using coef vs omit a group when compare 3 groups.
limma
13 days ago • updated 5 days ago
Chris
• 0
0
votes
2
replies
233
views
Odd behavior of Rsubread::featureCounts when setting `nonOverlap = 0`
featureCounts
Rsubread
23 days ago • updated 4 days ago
isaac.vock
• 0
15
votes
22
replies
1.8k
views
The difference when using Limma compare between 3 conditions vs 2 conditions
limma
25 days ago • updated 3 days ago
Chris
• 0
6
votes
5
replies
392
views
Estimating Cell Counts for EPIC V2 array data
FlowSorted.Blood.EPIC
minifi
written 7 weeks ago by
Kim
• 0
0
votes
7
replies
383
views
DESeq filtering specific to contrasts
DESeq2
updated 4 days ago by
Michael Love
41k • written 9 weeks ago by
Emma
• 0
0
votes
2
replies
763
views
Job:
Bioinformatics Laboratory Head in AI or machine learning (WEHI, Australia)
bioconductor
artificialintelligence
JobPosting
machinelearning
written 7 months ago by
Gordon Smyth
50k
5
votes
9
replies
1.2k
views
Batch correction and repeated measures
RUVSeq
sva
limma
updated 6 days ago by
Gordon Smyth
50k • written 7 months ago by
Jonathan
▴ 10
0
votes
18
replies
2.4k
views
problem installing ENmix package
ENmix
Bioconductor
rtracklayer
written 3.1 years ago by
lea
• 0
1
vote
7
replies
1.7k
views
Error using champ.import
ChAMP
EPICv2
updated 6 days ago by
shilpa
• 0 • written 9 months ago by
medha.suman
• 0
2
votes
5
replies
1.1k
views
DESeq2 remove batch effect
BatchEffect
RNASeqData
WGCNA
DESeq2
updated 6 days ago by
Ashley
• 0 • written 10 months ago by
zxc741xb
• 0
1
vote
2
replies
763
views
How to tell and visualize up/down regulation of pathways from clusterprofiler gsea output
clusterProfiler
RNASeq
updated 5 days ago by
sredemption
• 0 • written 13 months ago by
ruiqi.li
▴ 10
6
votes
10
replies
1.5k
views
Which input file is used for DGEList in EgdeR?
salmon
edgeR
tximport
nf-core
gene_counts
updated 4 days ago by
i.atanasoai
• 0 • written 14 months ago by
mohammedtoufiq91
▴ 10
0
votes
2
replies
884
views
Single-Cell Data Simulation from Bulk RNA-seq
SingleCell
RNASeq
RNASeqData
scRNAseq
updated 6 days ago by
wichaidi
• 0 • written 17 months ago by
irvin.ng
• 0
0
votes
2
replies
896
views
Problem for loading Bioconductor package in R
Bioconductor
written 4.2 years ago by
araaaju
• 0
6
votes
16
replies
2.2k
views
DESeq2 a lot of genes showing up as differentially expressed that only have 1 sample with any expression
deseq2
updated 18 hours ago by
Michael Love
41k • written 4.6 years ago by
hsbio
▴ 10
2
votes
5
replies
693
views
DESeq2 setting significant p-value
DESeq2
updated 4 days ago by
Michael Love
41k • written 5.0 years ago by
Merlin
▴ 10
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
5
votes
8
replies
8.7k
views
Limma design with continuous and categorical covariates
limma
batch effect
covariates
microarray
updated 1 day ago by
hortense96
• 0 • written 7.7 years ago by
dmcleanuk
▴ 30
9
votes
12
replies
7.8k
views
Multi factor design edgeR/Deseq2
deseq2
edgeR
rna-seq
updated 5 days ago by
Elizabeth
• 0 • written 8.8 years ago by
gthm
▴ 30
11
votes
5
replies
7.3k
views
Theoretical WGCNA Question
WGCNA
Theory
Scale-Free Topology
updated 5 days ago by
Garrett
• 0 • written 9.1 years ago by
brohawndg
▴ 150
77 results • Page
2 of 2
Recent ...
Replies
Comment: Different Shrunk Log2FC according with reference
by
andrebolerbarros
▴ 20
Thanks @atpoint for your answer! The issue with that is then it severely hinders the possiblity of using `apeglm` shrinking approach, sinc…
Comment: featureCounts reports an error:"featureCounts: input-files.c:2890: SAM_pairer_ge
by
ATpoint
★ 4.0k
The error that is relevant is `Aborted (core dumped)`. This line 2890 refers to the C source code that throws the error, it is not relevant…
Answer: Different Shrunk Log2FC according with reference
by
ATpoint
★ 4.0k
Please see: https://support.bioconductor.org/p/p134551/ I asked basically the same before. In short, reference level might have an influ…
Comment: Error for AnnotationForge makeOrgPackageFromNCBI function
by
Gayatri
• 0
What I meant is even after deleting the NCBI.sqlite file, and re-running the script, an empty NCBI.sqlite file (0 kb) is created which is c…
Comment: DESeq2 output used for PCA plot on R studio
by
ATpoint
★ 4.0k
> Increase variability for mutants: use larger subtractive modifiers I was thinking the same as swbarnes. You're doing some data munging h…
Votes
Subset DEXSeqDataSet In DEXSeq
How to get all possible comparisons in DiffBind
Comment: get BM error
Answer: Citation for edgeR user guide
Use of negative binomial model for exponential decay rate estimation using DESeq (or similar)
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Gordon Smyth
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i.sudbery
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