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24
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Splitting multiple groups - three different ages
DESeq2
12 hours ago
jd348
• 0
• updated just now
Michael Love
32k
0
votes
1
reply
24
views
Same methylation probe ID with different locus annotations in Illumina 27k and 450k plotforms
IlluminaHumanMethylation27kanno.ilmn12.hg19
12 hours ago
yuabrahamliu
• 0
• updated 5 minutes ago
Kevin Blighe
2.5k
0
votes
1
reply
12
views
DESeq2, tximport normalization, normalization factors, size factors
tximport
DESeq2
normalizationfactors
sizefactors
1 hour ago
svenbioinf
• 0
• updated 13 minutes ago
Michael Love
32k
2
votes
4
replies
33
views
Removing rows (countData) from a DESeq Object
DESeq2
3 hours ago • updated 1 hour ago
Bine
• 0
3
votes
1
reply
35
views
Using group instead of interaction term on a custom edited matrix
DESeq2
15 hours ago
jd348
• 0
• updated 14 hours ago
Michael Love
32k
1
vote
2
replies
44
views
Batch correction and DESeq2
DESeq2
19 hours ago
Alessia
• 0
• updated 15 hours ago
ATpoint
• 470
0
votes
0
replies
26
views
Can you colour dendrogram branch clusters in pheatmap?
R
heatmaps
pheatmap
1 day ago
trichorico
• 10
0
votes
1
reply
43
views
DMRcate extractRanges error
DMRcate
1 day ago
macsue.jacques
• 10
• updated 23 hours ago
shepherl
2.5k
1
vote
1
reply
46
views
Best way to handle tags of bam files
GenomicAlignments
bam
Rsamtools
1 day ago
changxu.fan
• 0
• updated 1 day ago
Martin Morgan
25k
0
votes
1
reply
38
views
Deseq2 Paired Samples Design
DESeq2
1 day ago
Rita
• 0
• updated 1 day ago
Michael Love
32k
0
votes
2
replies
79
views
Using edgeR and a spike-in to calculate absolute abundance
edgeR
SpikeIn
RNASeq
2 days ago
robert.chen
• 0
• updated 1 day ago
Gordon Smyth
42k
0
votes
1
reply
44
views
Produce quantile normalized expression values for use with BatchQC
BatchQC
2 days ago
Josh
• 0
• updated 1 day ago
Malcolm Cook
♦ 1.5k
0
votes
0
replies
30
views
tximport rowsum error
tximport
1 day ago
Ezgi
• 30
1
vote
1
reply
37
views
PCA rand heatmap of raw data
DESeq2
DiffSeq
PrincipalComponent
rlog
heatmaps
1 day ago
Fischer-philipp
• 30
• updated 1 day ago
Michael Love
32k
2
votes
3
replies
51
views
Single sided P-value for DESeq2 Likelihood Ratio Test
DESeq2
DESe
1 day ago
glennli
• 0
• updated 1 day ago
Michael Love
32k
0
votes
1
reply
51
views
DiffBind fragmentSize meaning
DiffBind
9 days ago
Jürgen
• 0
• updated 1 day ago
Rory Stark
♦ 3.6k
0
votes
4
replies
82
views
DiffBind analysis for ATAC-Seq error Error processing one or more read files
ATACSeq
DiffBind
6 days ago
Asma
• 0
• updated 1 day ago
Rory Stark
♦ 3.6k
0
votes
1
reply
45
views
ERROR: cannot finish the BAM file. Please check the disk space in the output directory.
Rsubread
1 day ago
Mehrad
• 0
• updated 1 day ago
Yang Liao
• 220
0
votes
3
replies
89
views
How to properly average normalized counts of biological replicates
DESeq2
Normalization
RNASeqR
3 days ago
Marina
• 0
• updated 14 hours ago
Michael Love
32k
3
votes
5
replies
91
views
DEseq2 results
heatmaps
DEGs
PCA
2 days ago
MOHAMMAD
• 0
• updated 21 hours ago
Kevin Blighe
2.5k
0
votes
1
reply
47
views
How to plot the RMA log2 normalised data from Affymetrix
log2
RMA
Affymetrix
affy
Normalization
3 days ago
Lara
• 0
• updated 2 days ago
Kevin Blighe
2.5k
0
votes
0
replies
32
views
ribosomeProfilingQC - countReads function - is it possible to consider library type - non-stranded, forward-stranded or rev-stransded?
ribosomeProfilingQC
countReads
3 days ago
alexandr.gopanenko
• 20
0
votes
2
replies
58
views
Error: Aesthetics must be either length 1 or the same as the data (1): x and xend
fgsea
3 days ago
yueli7
• 10
• updated 2 days ago
Kevin Blighe
2.5k
0
votes
2
replies
50
views
Error in library(oligo) : package or namespace load failed for ‘oligoClasses’
R
oligoClasses
Oligoclass
Bioconductor
Oligo
4 days ago
tanya
• 0
• updated 3 days ago
Martin Morgan
25k
0
votes
3
replies
113
views
Unable to upload an App in shinyapps.io with bioconductor packages
shinny
graph
RBGL
13 days ago
Xavier-Andoni
• 0
• updated 4 days ago
Marcel Ramos
490
1
vote
2
replies
79
views
Question about nearest function in R package IRanges
nearest
IRanges
4 days ago
junhui.li11
• 0
• updated 3 days ago
Julie Zhu
♦ 4.3k
1
vote
2
replies
60
views
How to install Ghostscript in windows?
RnBeads.hg19
RnBeads
4 days ago
Federica
• 0
0
votes
5
replies
1.0k
views
assayData: 0 features
geoquery
5.5 years ago
Ed Siefker
• 230
• updated 4 days ago
H. Zadeh
• 0
0
votes
2
replies
61
views
Pair-wise DESeq2 using tximport (running time and multi-threading)
tximport
DESeq2
5 days ago
Marcus
• 0
• updated 5 days ago
Michael Love
32k
0
votes
1
reply
53
views
Trouble Loading Data into Champ
loaddata
ChAMPdata
champload
R
ChAMP
7 days ago
Bethan
• 0
• updated 5 days ago
bastien.ducreux
• 0
3
votes
6
replies
181
views
Is it possible to create `HDF5Array` Delayed Arrays from HDF5 files hosted on S3?
TileDBArray
HDF5Array
MultiAssayExperiment
10 days ago • updated 4 days ago
Thomas Sandmann
• 80
1
vote
2
replies
57
views
error in DESeq2 results(dds)
DESeq2
datasetfrommatrix
results
error
5 days ago • updated 4 days ago
james
• 0
0
votes
0
replies
32
views
dmrseq on a subset of genomic regions
dmrseq
5 days ago
KIR_F
• 0
0
votes
1
reply
68
views
plotSex error message
minfiData
plotsex
minfi
minfiDataEPIC
r
6 days ago
Bethan
• 0
• updated 4 days ago
suman
• 0
0
votes
0
replies
27
views
iupac2meme function missing in universalmotif package
universalmotif
5 days ago
lessismore
• 0
0
votes
0
replies
25
views
combineTwoExpressionSet from a4Base is not working properly
a4Base
5 days ago
irene.roman
• 0
0
votes
0
replies
42
views
MEDIPS - export wig with normalized counts
MEDIPS
6 days ago
lshepard
• 40
2
votes
2
replies
63
views
makeTxDbFromUCSC("mm10", "refGene") gives "not supported" error
GenomicF
GenomicFeatures
6 days ago
erhoppe
• 0
2
votes
4
replies
79
views
How to launch the RnBeads Data Juggler?
RnBeads
6 days ago
Federica
• 0
1
vote
4
replies
73
views
goseq package loading issues
DESeq2
goseq
6 days ago • updated 5 days ago
avinashi
• 0
1
vote
1
reply
52
views
How to find the source code of the package STRINGdb ?
STRINGdb
Bioconductor
6 days ago
deepue
• 10
• updated 6 days ago
shepherl
2.5k
1
vote
2
replies
87
views
Regarding transcripts to gene ID conversion in tximport
salmon
tximport
DESeq2
7 days ago • updated 6 days ago
Nikolay Ivanov
• 0
0
votes
1
reply
53
views
error during installation of 'DEseq2' package
DESeq2
Install
7 days ago
su
• 0
• updated 17 hours ago
Hervé Pagès
14k
3
votes
2
replies
91
views
Why some statistically differently expressed genes are not DEGs?
RNASeqData
DEGreport
edgeR
7 days ago
Wuschel
• 10
2
votes
2
replies
69
views
How to download KEGG pathways for list of enriched genes
RNASeqRData
GO
7 days ago
Wuschel
• 10
2
votes
3
replies
83
views
DESeq2 extracting relevant contrasts with interactions
DESeq2
DifferentialExpression
7 days ago
jd348
• 0
• updated 6 days ago
Michael Love
32k
0
votes
1
reply
75
views
Using tximport to create the input for DESeq2
RNASeqR
7 days ago
ahmesalama
• 0
• updated 7 days ago
Michael Love
32k
0
votes
0
replies
51
views
ENmix: how to combine oxBS.MLE with RCP?
ENmix
7 days ago
joannew
• 0
0
votes
2
replies
72
views
How to setup sample design in DESeq2
DESeq2
7 days ago
dequattro.concetta
• 10
• updated 7 days ago
swbarnes2
• 640
5
votes
5
replies
124
views
analyzing RNA-Seq transcriptomic data (GEO accession: GSE96058)
GEO
RNASeqR
Transcriptomics
7 days ago
H. Zadeh
• 0
• updated 7 days ago
James W. MacDonald
56k
40,282 results • Page
1 of 806
Recent ...
Replies
Answer: Splitting multiple groups - three different ages
by
Michael Love
32k
It may be hard to tell in this plot because PC1 explains so much of the difference. The variability is not so stark as in other cases, and …
Answer: Same methylation probe ID with different locus annotations in Illumina 27k and 4
by
Kevin Blighe
2.5k
Hi, It seems that the manufacturer (Illumina) simply moved the target locus, which often occurs across array designs. In the case of c…
Answer: DESeq2, tximport normalization, normalization factors, size factors
by
Michael Love
32k
1) "counts(dds,normalized=TRUE)" returns counts that are corrected for library size and transcript length. Yes, and the indication is th…
Comment: DiffBind dba.report() output: Is "concentration" normalized?
by
Rory Stark
♦ 3.6k
As I understand it, you have two contrasts that share one group of samples. You expect the concentrations reported for the shared group to …
Comment: Removing rows (countData) from a DESeq Object
by
Bine
• 0
Thank you I will check this documentation!
Votes
Comment: DEseq2 results
Answer: Diffbind principal components
Comment: Removing rows (countData) from a DESeq Object
Comment: Removing rows (countData) from a DESeq Object
Answer: Using group instead of interaction term on a custom edited matrix
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