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15
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One error problem occurred caused by data type during using GDCprepare to handle BRCA data
GDCRNATools
TCGA
3 hours ago
glaciya2018
• 0
1
vote
2
replies
61
views
Reproducibility issue with scran together with lapply and BiocParallel
scran
BiocParallel
bluster
1 day ago • updated 3 hours ago
ATpoint
★ 4.0k
0
votes
2
replies
81
views
Opposite sign of LFC in count plots of DEGs (DESeq2)
DESeq2
1 day ago • updated 3 hours ago
winwater0928
• 0
0
votes
2
replies
101
views
featureCounts reports an error:"featureCounts: input-files.c:2890: SAM_pairer_get_next_read_BIN: Assertion `l_name < 256' failed. Aborted (core dumpe…
metaMSdata
2 days ago • updated 4 hours ago
shuwangxinze1996
• 0
0
votes
8
replies
194
views
DESeq2 output used for PCA plot on R studio
DESeq2
RSTUDIO
PCAtools
updated 5 hours ago by
swbarnes2
★ 1.3k • written 1 day ago by
Aaliya
• 0
0
votes
0
replies
20
views
PCA plot suggestions
DESeq2
PCAtools
7 hours ago
Aaliya
• 0
0
votes
1
reply
69
views
DESEQ2 IHW and Apelgm method for Shrinkage (adding s values to FDR)
DESeq2
RNAseq
updated 14 hours ago by
Michael Love
41k • written 17 hours ago by
kcarey
• 0
1
vote
13
replies
243
views
Trying to use enrichGO
clusterProfiler
GenomicDistributionsData
KEGG
3 days ago • updated 14 hours ago
fernanda.backsouza
▴ 10
0
votes
0
replies
16
views
ATACseq merge peaks
DiffBind
18 hours ago • updated 17 hours ago
Shloka
• 0
2
votes
5
replies
138
views
get BM error
ensembldb
updated 19 hours ago by
James W. MacDonald
65k • written 1 day ago by
Fara
• 0
0
votes
0
replies
15
views
Differential splicing from SGSeq analysis
DEXSeq
SGSeq
20 hours ago • updated 19 hours ago
Sara
• 0
0
votes
5
replies
208
views
Error for AnnotationForge makeOrgPackageFromNCBI function
OrgDb
AnnotationForge
updated 20 hours ago by
James W. MacDonald
65k • written 3 days ago by
Gayatri
• 0
2
votes
3
replies
98
views
How to retrieve gene ontology GO class from gene list?
GO.db
goTools
updated 21 hours ago by
James W. MacDonald
65k • written 1 day ago by
bandconductor
• 0
0
votes
0
replies
25
views
Exon-exon Junction Analysis for Variable-length Exons
Rsubread
22 hours ago
Dario Strbenac
★ 1.5k
1
vote
3
replies
82
views
Different Shrunk Log2FC according with reference
DESeq2
updated 22 hours ago by
Michael Love
41k • written 1 day ago by
andrebolerbarros
▴ 20
1
vote
3
replies
810
views
How to tell and visualize up/down regulation of pathways from clusterprofiler gsea output
clusterProfiler
RNASeq
updated 1 day ago by
Guangchuang Yu
★ 1.2k • written 13 months ago by
ruiqi.li
▴ 10
1
vote
4
replies
128
views
minfi::read.metharray.exp
minfiData
minfi
updated 1 day ago by
Basti
▴ 780 • written 2 days ago by
clacarion
• 0
2
votes
1
reply
162
views
Use of negative binomial model for exponential decay rate estimation using DESeq (or similar)
DESeq2
updated 1 day ago by
Michael Love
41k • written 1 day ago by
i.sudbery
▴ 40
1
vote
1
reply
68
views
Citation for edgeR user guide
edgeR
updated 1 day ago by
Gordon Smyth
50k • written 1 day ago by
k___
▴ 30
0
votes
7
replies
610
views
News:
List of Deprecated Packages for Bioc3.19
Release
Devel
ExperimentData
Software
7 weeks ago • updated 1 day ago
shepherl
3.8k
1
vote
1
reply
55
views
Cannabis OrgDb
KEGGgraph
org.Cs.eg.db
clusterProfiler
KEGG
AnnotationHubSoftware
updated 1 day ago by
James W. MacDonald
65k • written 1 day ago by
fernanda.backsouza
▴ 10
0
votes
0
replies
24
views
News:
Interested in the analysis of Spatial Omics data?
tidySpatialExperiment
SpatialExperiment
MoleculeExperiment
1 day ago
info
▴ 10
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 1 day ago by
Michael Love
41k • written 4.6 years ago by
hsbio
▴ 10
3
votes
3
replies
153
views
DESeq2 - dispersion estimation when there is none
DESeq2
updated 1 day ago by
Michael Love
41k • written 2 days ago by
WardDeb
• 0
0
votes
7
replies
240
views
Methylation Analysis experiment design using Limma
DNAMethylation
limma
methylationArrayAnalysis
8 days ago • updated 2 days ago
hortense96
• 0
5
votes
8
replies
8.8k
views
Limma design with continuous and categorical covariates
limma
batch effect
covariates
microarray
updated 2 days ago by
hortense96
• 0 • written 7.7 years ago by
dmcleanuk
▴ 30
1
vote
2
replies
923
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 2 days ago by
Tim Peters
▴ 170 • written 14 months ago by
jose.ramirez1
▴ 10
0
votes
1
reply
87
views
limma-voom: Calculate the log-fold change in gene expression within a sample
limma
RNASeq
voom
updated 2 days ago by
Gordon Smyth
50k • written 2 days ago by
taur.vil
• 0
1
vote
4
replies
142
views
Error EPICv2 ChAMP
ChAMPdata
IlluminaHumanMethylationEPICv2anno.20a1.hg38
ChAMP
updated 2 days ago by
James W. MacDonald
65k • written 6 days ago by
Mirella Aurora
• 0
4
votes
6
replies
325
views
FilterByExpr low counts with small sample size
edgeR
7 days ago • updated 2 days ago
Jonathan
▴ 10
0
votes
1
reply
80
views
FDR via q-value
qvalue
updated 2 days ago by
James W. MacDonald
65k • written 5 days ago by
John
• 0
6
votes
12
replies
4.7k
views
BiocFileCache/ExperimentHub/AnnotationHub temporary ERROR
BiocFileCache
AnnotationHub
ExperimentHub
6 months ago • updated 2 days ago
shepherl
3.8k
3
votes
2
replies
153
views
Cannabis and KEGGgraph
KEGGREST
GenomicDistributionsData
KEGGgraph
KEGG
updated 3 days ago by
Guido Hooiveld
★ 3.9k • written 5 days ago by
fernanda.backsouza
▴ 10
0
votes
2
replies
151
views
RNAseq:Technical replicates from different batches
technicalReplicates
BatchEffect
limma
RNASeq
5 days ago • updated 3 days ago
catv
• 0
0
votes
0
replies
41
views
Improving the design matrices vignette in RNAseq123
RNAseq123
3 days ago
Lluís Revilla Sancho
▴ 730
0
votes
3
replies
1.1k
views
News:
European Bioconductor Conference 2023 planning
Europe
Conference
EuroBioC
Events
News
updated 3 days ago by
lauryfriese932
• 0 • written 18 months ago by
Maria Doyle
▴ 70
12
votes
12
replies
756
views
Why p value inconsistent when using different number of pathway score?
limma
updated 3 days ago by
Robert Castelo
★ 3.3k • written 4 days ago by
Chris
• 0
0
votes
0
replies
39
views
Unlocking Potential: NURS FPX Strategies and Insights
levi
NURSFPX
ragene20sttranscriptcluster.db
ssrch
4 days ago
vaxahey107
• 0
3
votes
3
replies
283
views
permutation test in edgeR
rna-seq
edgeR
updated 4 days ago by
Gordon Smyth
50k • written 17 days ago by
Netanel
• 0
0
votes
18
replies
2.4k
views
problem installing ENmix package
ENmix
Bioconductor
rtracklayer
written 3.1 years ago by
lea
• 0
15
votes
22
replies
1.8k
views
The difference when using Limma compare between 3 conditions vs 2 conditions
limma
26 days ago • updated 4 days ago
Chris
• 0
0
votes
0
replies
61
views
I am trying to detect alternative splicing.
ASpli
4 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
764
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
194
views
Differential peaks that were not identified in diffbind were identified in diseq2
DiffBind
DESeq2
ATACSeq
7 days ago • updated 5 days ago
lonn
• 0
1
vote
2
replies
217
views
How to retrieve detailed regression results from deseq2
DESeq2
14 days ago • updated 5 days ago
Weiqian
▴ 10
1
vote
0
replies
198
views
Tutorial:
Installing/switching between versions of R/Rstudio/Bioconductor on personal machine (Linux | Ubuntu)
bioconductor
Install
5 days ago
BioinfGuru
▴ 30
0
votes
7
replies
386
views
DESeq filtering specific to contrasts
DESeq2
updated 5 days ago by
Michael Love
41k • written 9 weeks ago by
Emma
• 0
0
votes
2
replies
234
views
Odd behavior of Rsubread::featureCounts when setting `nonOverlap = 0`
featureCounts
Rsubread
24 days ago • updated 5 days ago
isaac.vock
• 0
0
votes
3
replies
100
views
Error retrieving ensembl gene id using biomaRt...
biomaRt
updated 5 days ago by
James W. MacDonald
65k • written 5 days ago by
bas_work
▴ 30
1,000 results • Page
1 of 20
Recent ...
Replies
Comment: Reproducibility issue with scran together with lapply and BiocParallel
by
ATpoint
★ 4.0k
Thanks Aaron for the response. RNGseed (for me) has no effect. I actually stumbled over this in one of my analysis where I have a constant …
Comment: Opposite sign of LFC in count plots of DEGs (DESeq2)
by
winwater0928
• 0
Thank you for your comment! 1)"Your contrast is comparing LGR5 to Homeostasis." means (Lgr5)/(Homeostasis). Is it right? Then, I think if…
Answer: Reproducibility issue with scran together with lapply and BiocParallel
by
Aaron Lun
★ 28k
IIRC **BiocParallel** switches to a different RNG when inside its own functions like `bplapply` - specifically L'Ecuyer-CMRG, as opposed to…
Comment: DESeq2 output used for PCA plot on R studio
by
swbarnes2
★ 1.3k
This looks terrible for RNASeq data, because it's not RNASeq data. It's a matrix of pretty random numbers, which you know because you poste…
Comment: DESeq2 output used for PCA plot on R studio
by
Aaliya
• 0
I had taken this code from internet, but after reading about it and I did on my own, I would be making a post to ask for the suggestions if…
Votes
C: null model and DEXSeqDataSet object in DEXSEQ
A: Are published RNA seq data analyses often wrong in calculating p-values and FDR?
A: How to explain how DESeq2 works to someone with zero bioinformatics background?
Answer: Interpret plot from DiffBind
Answer: How to retrieve gene ontology GO class from gene list?
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