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Check removeBatchEffect effectiveness
RNAseq
limma
removeBatchEffect
updated 4 hours ago by
ATpoint
★ 4.8k • written 20 hours ago by
massimo
• 0
0
votes
0
replies
77
views
Significant Probes and Genes differ in Probe and Region level Differential Methylation Analyses
limma
probe
DMRcate
GenomicRanges
DifferentialMethylation
1 day ago
jamiecatalano2
• 0
0
votes
3
replies
734
views
CluserProfiler message "No gene can be mapped"
clusterProfiler
updated 2 days ago by
James W. MacDonald
68k • written 4 days ago by
Carolina
• 0
0
votes
1
reply
90
views
Filtering after DESeq
DESeq2
IHW
updated 4 hours ago by
ATpoint
★ 4.8k • written 2 days ago by
caroline.zanchi
• 0
0
votes
1
reply
216
views
RNA-seq input to GRaNIE
GRaNIE
updated 3 days ago by
James W. MacDonald
68k • written 4 days ago by
maia.malonzo
• 0
0
votes
1
reply
470
views
Help using reduceSimMatrix with a custom annotation
AnnotationHub
GOSemSim
rrvgo
updated 3 days ago by
sergisayolspuig
▴ 80 • written 5 months ago by
daccar98
• 0
0
votes
1
reply
220
views
Analyzing TnSeq data with DESeq2
DESeq2
updated 4 days ago by
cold.wolverine.arku
• 0 • written 4 days ago by
Lynn
• 0
1
vote
5
replies
1.4k
views
Package developing and interoperation with Bioconductor
Package
Bioconductor
written 4 weeks ago by
slizchap
• 0
0
votes
0
replies
44
views
How to left_join a tidySummarizedExperiment with a GRanges object by seqnames and start (tidyverse-style)?
GenomicRanges
tidySummarizedExperiment
tidyomics
5 days ago
Kateřina
• 0
0
votes
6
replies
1.7k
views
News:
EuroBioC2024 abstract submission is open!
Conference
Bioconductor
EuroBioC2024
written 14 months ago by
Maria Doyle
▴ 100
2
votes
1
reply
388
views
ROAST for small sets
limma
mroast
updated 5 days ago by
Gordon Smyth
52k • written 5 days ago by
Jay
• 0
0
votes
1
reply
612
views
How do I set up my DESeq analysis when I know a few vehicle control samples provide background effects we don't want to see in any of the subsequent …
DESeq2
RUVSeq
updated 5 days ago by
Michael Love
43k • written 4 weeks ago by
Simran
• 0
0
votes
2
replies
450
views
Differing results with DESeq2
DESeq2
updated 3 days ago by
JKim
• 0 • written 23 days ago by
hampsdiv
• 0
0
votes
1
reply
84
views
Make DEXSeq plot normal scale
DEXSeq
Dexseq
updated 5 days ago by
James W. MacDonald
68k • written 6 days ago by
Rico
• 0
0
votes
2
replies
311
views
RNA Seq using Lrt
DESeq2
6 days ago • updated 4 days ago
Rob
• 0
10
votes
13
replies
1.7k
views
edgeR::cpm() results in negative values from raw counts of 0
edgeR
updated 4 days ago by
Gordon Smyth
52k • written 6 days ago by
Kinnary
▴ 20
0
votes
2
replies
415
views
Gene Ontology (GO) Analysis
GOstats
hyperGTest
GO
enrichGO
clusterProfiler
updated 1 day ago by
Tom
• 0 • written 8 days ago by
GA
▴ 10
0
votes
0
replies
63
views
Batch correction for microarray
BatchEffect
sva
MicroarrayData
7 days ago
Shaimaa Gamal
• 0
5
votes
9
replies
1.9k
views
Feature Counts - potential bug with outfile.jcounts
featurecounts
Rsubread
updated 9 days ago by
Wei Shi
★ 3.6k • written 4 months ago by
chris2.a.white
• 0
0
votes
0
replies
49
views
GRaNIE with no internet
GRaNIE
10 days ago
maia.malonzo
• 0
0
votes
5
replies
2.2k
views
Aclust package: IlluminaHumanMethylation450kCHR37 not found
illuminahumanmethylation450k.db
aclust
methylation
annotation
illumina
written 8.7 years ago by
aagata.szymanek
• 0
2
votes
0
replies
405
views
News:
Bioconductor 3.21 is Released!
devel
release
Release
Devel
11 days ago
shepherl
4.1k
0
votes
1
reply
577
views
Version conflict when pushing to scQTLtools devel branch
Bioconductor
updated 11 days ago by
shepherl
4.1k • written 11 days ago by
XFWu
• 0
0
votes
0
replies
55
views
Issue checking for convergence with the tutorial Dataset. EBseq 2.4.1
EBSeq
12 days ago
Javier
• 0
1
vote
9
replies
3.0k
views
DiffBind - question on the use of filtered or unfiltered input data
DiffBind
written 2.0 years ago by
Oscar
▴ 10
0
votes
3
replies
717
views
Log2foldchange strange behavior
DESeq2
updated 13 days ago by
ATpoint
★ 4.8k • written 14 days ago by
RambakKulit
• 0
0
votes
1
reply
537
views
WGCNA
WGCNA
DESeq2
updated 16 days ago by
ATpoint
★ 4.8k • written 20 days ago by
bioinformaticssrm2011
• 0
0
votes
2
replies
567
views
cannot download atena annotation for human
atena
updated 16 days ago by
Robert Castelo
★ 3.4k • written 8 weeks ago by
Davide
• 0
0
votes
1
reply
829
views
Comparison of results obtained from a subset of the data versus the complete dataset for a few selected genes.
DESeq2
updated 16 days ago by
swbarnes2
★ 1.4k • written 17 days ago by
Bioinformatician_R
▴ 20
0
votes
0
replies
131
views
I want my overlapping peaks to stop merging by default doing read counting (using DiffBind in R-studio)
peakoverlap
mergingpeaks
ChIPseq
DiffBind
17 days ago
atlanta
• 0
1
vote
1
reply
1.1k
views
PhD scholar
RNASeqAnalysis
DESeq2
updated 16 days ago by
shepherl
4.1k • written 17 days ago by
Richa
• 0
2
votes
3
replies
1.4k
views
how to use `arrayWeightsQuick()`?
limma
updated 17 days ago by
Gordon Smyth
52k • written 18 days ago by
matthew
• 0
1
vote
1
reply
996
views
Differential expression analysis using two TCGA datasets
DifferentialExpression
TCGAbiolinks
RNASeq
updated 17 days ago by
ATpoint
★ 4.8k • written 17 days ago by
Shaimaa Gamal
• 0
1
vote
4
replies
807
views
fast apply on RleList
GenomicRanges
RleList
18 days ago • updated 17 days ago
story.benjamin
▴ 20
0
votes
1
reply
231
views
Custom CDF creation for HTA 2.0 array using GTF annotation
oligo
oligoClasses
pdInfoBuilder
affycoretools
affyio
18 days ago • updated 17 days ago
Seymoo
• 0
0
votes
8
replies
1.5k
views
Deleted:No significant MVPs with a BH adjusted P-value below 0.05
ChAMP
written 17 months ago by
486342583
• 0
3
votes
5
replies
812
views
BiocParallel_1.40.1.tar.gz not available
BiocParallel
19 days ago • updated 17 days ago
Johan
• 0
1
vote
0
replies
379
views
Modelling gene program dynamics across time with {lemur}
lemur
18 days ago • updated 16 days ago
BiotechPedro
▴ 10
1
vote
7
replies
2.3k
views
DNAStringSet(x, start=, end=) loses quality information
Biostrings
updated 18 days ago by
stenlana035
• 0 • written 3.4 years ago by
Gerhard Thallinger
▴ 180
0
votes
1
reply
309
views
Intepretation of results
AUCell
updated 1 day ago by
Tom
• 0 • written 19 days ago by
jasperwong_123
• 0
0
votes
2
replies
476
views
Model performance for spline modelling of RNA-seq timecourses in edgeR
edgeR
limma
updated 15 days ago by
Gordon Smyth
52k • written 19 days ago by
skiaphrene
▴ 10
0
votes
1
reply
287
views
DESeq2 - am I extracting results incorrectly?
DESeq2
updated 19 days ago by
James W. MacDonald
68k • written 20 days ago by
bd2000
▴ 30
2
votes
1
reply
859
views
Having Trouble Using CNE12() and CNE21() in CNEr
GenomicRanges
CNEr
20 days ago
1324087964
• 0
1
vote
1
reply
1.4k
views
Origin of the labels for the SingleCellMultiModal dataset
labels
PBMC
SingleCellMultiModal
10X
updated 20 days ago by
ATpoint
★ 4.8k • written 20 days ago by
javier.ruizramirez
• 0
0
votes
4
replies
2.0k
views
DiffBind can't find a DAR
dar
ATACSeq
DiffBind
20 days ago • updated 10 days ago
Mengjun
• 0
1
vote
3
replies
784
views
DESeq - help with pair wise comparisons
DESeq2
20 days ago
bd2000
▴ 30
0
votes
0
replies
25
views
Spam:
Looking for Josey Wales Jacket?
MethylSeekR
23 days ago
Shoqz
0
1
vote
8
replies
2.5k
views
DESeq: Gene is not flagged as differentially expressed despite count data showing differences
DifferentialExpression
DESeq2
23 days ago • updated 20 days ago
ktz
• 0
0
votes
3
replies
906
views
compute_fasta_digest does not match Salmon index hash
tximeta
updated 14 days ago by
Michael Love
43k • written 4 weeks ago by
Alex
• 0
0
votes
0
replies
87
views
News:
Introduction to Epigenomics data analysis with R and Bioconductor course (online) - 14th-18th April
chipseq
MNaseSeq
ATACSeq
25 days ago • updated 21 days ago
info
▴ 10
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Comment: Bioconductor 3.20 Release Schedule
by
randyprice13102000
• 0
This offers much info https://bioconductor.org/checkResults/release/bioc-LATEST/
Comment: Filtering after DESeq
by
ATpoint
★ 4.8k
The problem is that your prefilter is not group-aware so the behaviour of seeing these sorts of outliers is expected. This is why I always …
Comment: GSEA preranked analysis downstream of DEseq2
by
ATpoint
★ 4.8k
All due respect, this is what people do since pvalues exist, so this paper is not a reference, not is this a special score that merits a na…
Comment: Check removeBatchEffect effectiveness
by
ATpoint
★ 4.8k
> insert size, mean GC, etc... This is not a classical "batch" in the common sense, at least I've never seen this to be corrected for expl…
Answer: Check removeBatchEffect effectiveness
by
Gordon Smyth
52k
Your call to removeBatchEffect() is not correct because that function does not have an argument called `batch3`, meaning that the batch fac…
Votes
Answer: DiffBind; Error: No sites have activity greater than filter value
DiffBind; Error: No sites have activity greater than filter value
remove X and Y chromosome genes in RNA-seq data using DESeq2 pipeline
How to remove X & Y chromosome genes from RNAseq data
Is it advisable to remove X and Y chromosome genes in mouse bulk RNA-seq data at the level of the count matrix?
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