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0
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0
replies
1.3k
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Venn diagrams using ChIPpeakAnno
annotate
ChIPpeakAnno
annotate
ChIPpeakAnno
12.5 years ago
Julie Zhu
★ 4.3k
0
votes
1
reply
1.3k
views
Comparing log FC edgeR
updated 12.5 years ago by
Gordon Smyth
53k • written 12.5 years ago by
Alpesh Querer
▴ 220
0
votes
2
replies
2.4k
views
romer implementation in edgeR
limma
edgeR
CAMERA
limma
edgeR
CAMERA
updated 12.5 years ago by
Gordon Smyth
53k • written 12.5 years ago by
Pekka Kohonen
▴ 190
0
votes
1
reply
2.7k
views
edgeR dispersion value
Homo sapiens
Homo sapiens
updated 12.5 years ago by
Mark Robinson
▴ 880 • written 12.5 years ago by
Guest User
★ 13k
0
votes
2
replies
1.3k
views
Flow Cytometry Analysis with FlowCore
updated 12.5 years ago by
Jiang, Mike
▴ 20 • written 12.5 years ago by
Guest User
★ 13k
1
vote
2
replies
1.5k
views
Study design in DEXSeq
Genetics
DEXSeq
Genetics
DEXSeq
updated 12.5 years ago by
Alejandro Reyes
★ 1.9k • written 12.5 years ago by
António Miguel de Jesus Domingues
▴ 510
0
votes
0
replies
1.2k
views
Problem running pathview due to broken XML package
GO
pathview
GO
pathview
12.5 years ago
Luo Weijun
★ 1.6k
0
votes
0
replies
1.5k
views
Identifying expression trends in RNA-seq experiment - through edgeR
edgeR
DOSE
edgeR
DOSE
12.5 years ago
Sandhya Pemmasani Kiran
▴ 40
0
votes
2
replies
2.8k
views
Disparity between MethylLumiSet (methylumi) and RGChannelSet (minfi) - treatment of missing values
probe
methylumi
probe
methylumi
updated 12.5 years ago by
Kasper Daniel Hansen
★ 6.5k • written 12.5 years ago by
Pilling, Luke
▴ 20
0
votes
5
replies
1.4k
views
graph::edgeMatrix() fails for signature(object="graphBAM")
updated 12.5 years ago by
Paul Shannon
▴ 470 • written 12.5 years ago by
Robert Castelo
★ 3.4k
0
votes
3
replies
2.2k
views
org.Hs.eg.db namespace issue
updated 12.5 years ago by
Dan Tenenbaum
▴ 60 • written 12.5 years ago by
Anthony Bosco
▴ 500
0
votes
1
reply
3.1k
views
Start and End positions in the GTF/GFF3 files
updated 12.5 years ago by
Hervé Pagès
16k • written 12.5 years ago by
Delasa Aghamirzaie
▴ 70
0
votes
4
replies
1.9k
views
read.ilmn() and variation between chips
Microarray
Normalization
probe
limma
Microarray
Normalization
probe
limma
updated 12.5 years ago by
Gordon Smyth
53k • written 12.5 years ago by
Rao,Xiayu
▴ 550
0
votes
3
replies
1.5k
views
technical + biological replicate design for multiple categories
limma
limma
12.5 years ago
James Platt
▴ 20
0
votes
3
replies
3.7k
views
Use which method to calculate q-value or adjusted p-value
updated 12.5 years ago by
Tim Triche
★ 4.2k • written 12.5 years ago by
Feng Tian
▴ 110
0
votes
1
reply
535
views
RJpGene.1.0 and RCnGene.1.0 .CDF files
cdf
affy
cdf
affy
updated 12.5 years ago by
James W. MacDonald
68k • written 12.5 years ago by
Guest User
★ 13k
0
votes
1
reply
1.1k
views
What is the FDR set to for the BH method.
Microarray
Microarray
updated 12.5 years ago by
Naomi Altman
★ 6.0k • written 12.5 years ago by
Cornish, Joseph NIH/NIAID [F]
▴ 50
0
votes
0
replies
783
views
merging two data frames
12.5 years ago
chris Jhon
▴ 260
0
votes
0
replies
1.2k
views
getting genotypes with oligo package
SNP
oligo
crlmm
SNP
oligo
crlmm
12.5 years ago
Guest User
★ 13k
0
votes
1
reply
4.1k
views
How to create a heatmap of a gene family (using subset of exprs(vsd) in DESeq)
DESeq
DESeq
updated 12.5 years ago by
Wolfgang Huber
★ 13k • written 12.5 years ago by
Guest User
★ 13k
0
votes
3
replies
2.1k
views
Merging two data frame
Cancer
Cancer
updated 12.5 years ago by
Steve Lianoglou
★ 13k • written 12.5 years ago by
chris Jhon
▴ 260
0
votes
1
reply
2.4k
views
Illumina Probe_ID used in the LIMMA package for neqc function
Microarray
Annotation
probe
limma
Microarray
Annotation
probe
limma
updated 12.5 years ago by
Wei Shi
★ 3.6k • written 12.5 years ago by
William D'Avigdor
▴ 40
0
votes
2
replies
2.4k
views
Question about mget vs. select for annotation package
hgu133plus2
probe
hgu133plus2
probe
updated 12.5 years ago by
Hervé Pagès
16k • written 12.5 years ago by
Christina Chaivorapol
▴ 40
0
votes
0
replies
911
views
limma: tissue specific genes using voom
12.5 years ago
Jaaved Mohammed
▴ 30
0
votes
2
replies
1.3k
views
IlluminaHumanMethylation450k.db: Missing probes in IlluminaHumanMethylation450kPROBELOCATION function?
updated 12.5 years ago by
VSM
▴ 120 • written 12.5 years ago by
Ed Schwalbe
▴ 10
0
votes
17
replies
3.7k
views
IlluminaHumanMethylation450k.db: Missing probes in IlluminaHumanMethylation450kPROBELOCATION function?
Microarray
illuminaHumanv2
Microarray
illuminaHumanv2
updated 12.5 years ago by
Tim Triche
★ 4.2k • written 12.5 years ago by
Simone
▴ 190
0
votes
1
reply
1.9k
views
problem with 'FDb.InfiniumMethylation.hg19'
BSgenome
BSgenome
lumi
methylumi
BSgenome
BSgenome
lumi
methylumi
updated 12.5 years ago by
VSM
▴ 120 • written 12.5 years ago by
James W. MacDonald
68k
0
votes
2
replies
1.1k
views
using a gtf file to map reads
GO
GenomicFeatures
DEXSeq
GO
GenomicFeatures
DEXSeq
updated 12.5 years ago by
Alejandro Reyes
★ 1.9k • written 12.5 years ago by
Valerie Obenchain
★ 6.8k
0
votes
1
reply
1.1k
views
rtracklayer
updated 12.5 years ago by
James W. MacDonald
68k • written 12.5 years ago by
Johannes Waage
▴ 30
0
votes
8
replies
7.8k
views
PCA-3D Plot
updated 12.5 years ago by
James W. MacDonald
68k • written 12.5 years ago by
Guest User
★ 13k
0
votes
0
replies
2.3k
views
info on pathview
graph
PROcess
pathview
graph
PROcess
pathview
12.5 years ago
Luo Weijun
★ 1.6k
0
votes
0
replies
767
views
sample probe profile or sample gene profile
Microarray
probe
Microarray
probe
12.5 years ago
Guest User
★ 13k
0
votes
0
replies
950
views
Gene expression clustering using several dependent samples
Clustering
affy
Clustering
affy
12.5 years ago
Moritz Kebschull
▴ 100
0
votes
0
replies
1.6k
views
BioC 2013, July 17 (Developer Day) 18-19: 'Early' registration deadline July 1
Cheminformatics
Visualization
Cancer
Ovarian
DEXSeq
minfi
DESeq2
BaseSpaceR
epivizr
minfi
12.5 years ago
Martin Morgan
25k
1
vote
4
replies
1.8k
views
problems running DEXseq
DEXSeq
DEXSeq
updated 12.5 years ago by
Steve Lianoglou
★ 13k • written 12.5 years ago by
Diya
▴ 10
0
votes
1
reply
945
views
pulling out specific lines from a bam file
SNP
SNP
updated 12.5 years ago by
Martin Morgan
25k • written 12.5 years ago by
Guest User
★ 13k
0
votes
0
replies
762
views
targets frame
limma
limma
12.5 years ago
Guest User
★ 13k
0
votes
2
replies
1.2k
views
Limma design for single channel arrays with technical repeats
updated 12.5 years ago by
Gordon Smyth
53k • written 12.6 years ago by
Giulio Di Giovanni
▴ 10
0
votes
1
reply
1.8k
views
RNA-seq: interaction effect with DESeq
DESeq
DESeq
12.5 years ago
galeb abu-ali
▴ 20
0
votes
3
replies
1.2k
views
read.ilmn() and variation between chips
Microarray
Normalization
limma
Microarray
Normalization
limma
updated 12.5 years ago by
Gordon Smyth
53k • written 12.6 years ago by
Rao,Xiayu
▴ 550
0
votes
0
replies
722
views
problem with 'FDb.InfiniumMethylation.hg19'
12.5 years ago
VSM
▴ 120
0
votes
4
replies
1.6k
views
test for differential expresssion
updated 12.5 years ago by
Gordon Smyth
53k • written 12.6 years ago by
Rao,Xiayu
▴ 550
3
votes
5
replies
3.5k
views
edgeR multiple contrasts Vs. One test
edgeR
edgeR
updated 12.5 years ago by
Gordon Smyth
53k • written 12.6 years ago by
Michael Breen
▴ 380
0
votes
2
replies
1.7k
views
lumiR returns ExpressionSet object instead of LumiBatch
GO
Mus musculus
BSgenome
BSgenome
lumi
GO
Mus musculus
BSgenome
BSgenome
lumi
updated 12.5 years ago by
Pan Du
▴ 440 • written 12.6 years ago by
Guest User
★ 13k
0
votes
4
replies
1.8k
views
Pathview published in Bioinformatics
Visualization
pathview
Visualization
pathview
12.6 years ago
Luo Weijun
★ 1.6k
0
votes
0
replies
1.8k
views
How to filter genes not expressed in all arrays using limma (single channel agilent microarray data)
Microarray
Microarray
12.6 years ago
Guest User
★ 13k
0
votes
2
replies
1.9k
views
limma: tissue specific genes using voom
RNASeq
limma
edgeR
RNASeq
limma
edgeR
updated 12.6 years ago by
Gordon Smyth
53k • written 12.6 years ago by
Jaaved Mohammed
▴ 30
0
votes
3
replies
2.3k
views
Regarding extraction of 3' and 5'UTRs and exonic region of a gene.
Cancer
Cancer
updated 12.6 years ago by
Hervé Pagès
16k • written 12.6 years ago by
abdul rawoof
▴ 60
0
votes
4
replies
6.2k
views
edgeR - ANOVA-like test for differential gene expression
RNASeq
edgeR
RNASeq
edgeR
12.6 years ago
Benedikt Drosse
▴ 30
0
votes
1
reply
1.1k
views
PREDA command does not work
PREDA
PREDA
updated 12.6 years ago by
Valerie Obenchain
★ 6.8k • written 12.6 years ago by
Guest User
★ 13k
46,712 results • Page
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Comment: Incosistencies in buildSNNGraph() function
by
ATpoint
★ 5.0k
Just played with this a bit and I think it comes down to not having a fixed seed before running the leiden thingy. Same goes for PCA and UM…
Answer: Incosistencies in buildSNNGraph() function
by
Aaron Lun
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The most obvious thing that comes to mind is the RNG seed. `cluster_leiden()` does some random number generation, somewhere deep in the **i…
Comment: Opportunity to host EuroBioC2026 Preconference workshops!
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Thank you for sharing the EuroBioC2026 workshop opportunity. I m interested in hosting a hands on session teaching reproducible data analys…
Comment: Ensembl plants at annotationHub?
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• 0
Nope I don't mind haha! Anyway thanks so much! Thats super kind of you!
Answer: Combining two proteomics datasets with limpa
by
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53k
Hi Andrew, We don't have that much experience combining different datasets with limpa yet, but my feeling is that the same DPC should be u…
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Answer: Incosistencies in buildSNNGraph() function
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limma moderated t-statistics and B-statistics
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