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0
votes
2
replies
46
views
Same methylation probe ID with different locus annotations in Illumina 27k and 450k plotforms
IlluminaHumanMethylation27kanno.ilmn12.hg19
1 day ago • updated 20 minutes ago
yuabrahamliu
• 0
0
votes
8
replies
58
views
problem installing ENmix package
ENmix
Bioconductor
rtracklayer
11 hours ago
lea
• 0
• updated 4 hours ago
James W. MacDonald
56k
1
vote
0
replies
19
views
News:
SBGNview: Data Analysis, Integration and Visualization on 5000+ Pathways/3000+ Species
SBGN
SBGNview
pathways
pathview
visualization
5 hours ago
Luo Weijun
♦ 1.5k
1
vote
5
replies
992
views
DiffBind dba.report() output: Is "concentration" normalized?
DiffBind
3.8 years ago
roman.hillje
• 0
• updated 7 hours ago
amwa
• 0
0
votes
1
reply
27
views
Diffbind error while running example data
DiffBind
11 hours ago
Lucky
• 0
• updated 9 hours ago
Rory Stark
♦ 3.6k
1
vote
3
replies
71
views
Best way to handle tags of bam files
GenomicAlignments
bam
Rsamtools
1 day ago • updated 9 hours ago
changxu.fan
• 0
0
votes
0
replies
19
views
How to get illumina CpG IDs by gene name?
MethylationArrayData
RnBeads
12 hours ago
D
• 0
0
votes
1
reply
43
views
Can you colour dendrogram branch clusters in pheatmap?
R
heatmaps
pheatmap
1 day ago
trichorico
• 10
• updated 14 hours ago
Kevin Blighe
2.5k
2
votes
1
reply
37
views
Splitting multiple groups - three different ages
DESeq2
1 day ago
jd348
• 0
• updated 14 hours ago
Michael Love
32k
0
votes
1
reply
29
views
DESeq2, tximport normalization, normalization factors, size factors
tximport
DESeq2
normalizationfactors
sizefactors
15 hours ago
svenbioinf
• 0
• updated 14 hours ago
Michael Love
32k
2
votes
4
replies
62
views
Removing rows (countData) from a DESeq Object
DESeq2
17 hours ago • updated 16 hours ago
Bine
• 0
3
votes
1
reply
45
views
Using group instead of interaction term on a custom edited matrix
DESeq2
1 day ago
jd348
• 0
• updated 1 day ago
Michael Love
32k
0
votes
3
replies
91
views
How to properly average normalized counts of biological replicates
DESeq2
Normalization
RNASeqR
4 days ago
Marina
• 0
• updated 1 day ago
Michael Love
32k
1
vote
2
replies
55
views
Batch correction and DESeq2
DESeq2
1 day ago
Alessia
• 0
• updated 1 day ago
ATpoint
• 470
0
votes
1
reply
54
views
error during installation of 'DEseq2' package
DESeq2
Install
7 days ago
su
• 0
• updated 1 day ago
Hervé Pagès
14k
3
votes
7
replies
232
views
Which version of R to use for "HiCDCPlus" "HiC-DC+"
HiC-DC+
HiCDCPlus
BiocParallel
3 months ago
Tay
• 10
• updated 1 day ago
koushik
• 0
4
votes
5
replies
101
views
DEseq2 results
heatmaps
DEGs
PCA
2 days ago
MOHAMMAD
• 0
• updated 1 day ago
Kevin Blighe
2.5k
0
votes
8
replies
528
views
Thoughts on computer purchase
14.9 years ago
Lance Palmer
• 60
• updated 1 day ago
Suji_
• 0
0
votes
5
replies
422
views
EdgeR: Filtering Counts Causes No Significance.
edger
22 months ago
bio.erikson
• 0
• updated 1 day ago
katieviljoen
• 0
1
vote
1
reply
55
views
DMRcate extractRanges error
DMRcate
1 day ago
macsue.jacques
• 10
• updated 1 day ago
shepherl
2.5k
0
votes
1
reply
42
views
Deseq2 Paired Samples Design
DESeq2
2 days ago
Rita
• 0
• updated 2 days ago
Michael Love
32k
0
votes
2
replies
82
views
Using edgeR and a spike-in to calculate absolute abundance
edgeR
SpikeIn
RNASeq
3 days ago
robert.chen
• 0
• updated 2 days ago
Gordon Smyth
42k
0
votes
1
reply
46
views
Produce quantile normalized expression values for use with BatchQC
BatchQC
3 days ago
Josh
• 0
• updated 2 days ago
Malcolm Cook
♦ 1.5k
0
votes
1
reply
49
views
ERROR: cannot finish the BAM file. Please check the disk space in the output directory.
Rsubread
2 days ago
Mehrad
• 0
• updated 2 days ago
Yang Liao
• 220
0
votes
0
replies
34
views
tximport rowsum error
tximport
2 days ago
Ezgi
• 30
1
vote
1
reply
43
views
PCA rand heatmap of raw data
DESeq2
DiffSeq
PrincipalComponent
rlog
heatmaps
2 days ago
Fischer-philipp
• 30
• updated 2 days ago
Michael Love
32k
2
votes
3
replies
59
views
Single sided P-value for DESeq2 Likelihood Ratio Test
DESeq2
DESe
2 days ago
glennli
• 0
• updated 2 days ago
Michael Love
32k
1
vote
1
reply
54
views
DiffBind fragmentSize meaning
DiffBind
10 days ago
Jürgen
• 0
• updated 2 days ago
Rory Stark
♦ 3.6k
0
votes
3
replies
99
views
DiffBind analysis on ChIP-Seq qata and design matrix
ChIPSeq
DiffBind
ExperimentalDesign
21 days ago
SFn
• 0
• updated 2 days ago
Rory Stark
♦ 3.6k
0
votes
4
replies
84
views
DiffBind analysis for ATAC-Seq error Error processing one or more read files
ATACSeq
DiffBind
7 days ago
Asma
• 0
• updated 2 days ago
Rory Stark
♦ 3.6k
0
votes
3
replies
1.9k
views
How do I choose between using affy or oligo package for preprocessing microarrays?
microarray
affymetrix microarrays
affy
oligo
4.1 years ago
stevessheridan
• 0
• updated 2 days ago
James W. MacDonald
56k
0
votes
2
replies
120
views
HiCDCPlus / HiC-DC+ is not found
HiCDCPlus
HiC-DC+
HiCcompare
HiC
3 months ago
mtS
• 0
• updated 2 days ago
merve.sahn
• 0
1
vote
5
replies
128
views
Swish (fishpond) scaled counts result
Swish
fishpond
28 days ago • updated 2 days ago
675743
• 10
2
votes
3
replies
72
views
Running old packages on Mac
ShortRead
14 days ago
Daniel.Berner@unibas.ch
• 90
1
vote
2
replies
61
views
How to install Ghostscript in windows?
RnBeads.hg19
RnBeads
5 days ago
Federica
• 0
0
votes
2
replies
59
views
Error: Aesthetics must be either length 1 or the same as the data (1): x and xend
fgsea
4 days ago
yueli7
• 10
• updated 3 days ago
Kevin Blighe
2.5k
0
votes
1
reply
48
views
How to plot the RMA log2 normalised data from Affymetrix
log2
RMA
Affymetrix
affy
Normalization
4 days ago
Lara
• 0
• updated 3 days ago
Kevin Blighe
2.5k
0
votes
0
replies
36
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
1
vote
2
replies
72
views
How to define settings for design primers with openPrimeR?
openPrimeR
9 days ago • updated 3 days ago
marongiu.luigi
• 0
1
vote
2
replies
79
views
Question about nearest function in R package IRanges
nearest
IRanges
5 days ago
junhui.li11
• 0
• updated 4 days ago
Julie Zhu
♦ 4.3k
0
votes
2
replies
51
views
Error in library(oligo) : package or namespace load failed for ‘oligoClasses’
R
oligoClasses
Oligoclass
Bioconductor
Oligo
4 days ago
tanya
• 0
• updated 4 days ago
Martin Morgan
25k
1
vote
3
replies
294
views
log2FC calculation in EdgeR
edger
log2FC
16 months ago
matteo.buti
• 0
3
votes
6
replies
182
views
Is it possible to create `HDF5Array` Delayed Arrays from HDF5 files hosted on S3?
TileDBArray
HDF5Array
MultiAssayExperiment
11 days ago • updated 4 days ago
Thomas Sandmann
• 80
0
votes
3
replies
114
views
Unable to upload an App in shinyapps.io with bioconductor packages
shinny
graph
RBGL
13 days ago
Xavier-Andoni
• 0
• updated 5 days ago
Marcel Ramos
490
0
votes
5
replies
1.0k
views
assayData: 0 features
geoquery
5.5 years ago
Ed Siefker
• 230
• updated 5 days ago
H. Zadeh
• 0
5
votes
3
replies
1.7k
views
GEOquery: 0 features in the gset object
geoquery
5.6 years ago
alakatos
• 110
• updated 5 days ago
H. Zadeh
• 0
1
vote
2
replies
60
views
error in DESeq2 results(dds)
DESeq2
datasetfrommatrix
results
error
5 days ago
james
• 0
0
votes
1
reply
68
views
plotSex error message
minfiData
plotsex
minfi
minfiDataEPIC
r
6 days ago
Bethan
• 0
• updated 5 days ago
suman
• 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
8 days ago
Bethan
• 0
• updated 5 days ago
bastien.ducreux
• 0
40,286 results • Page
1 of 806
Recent ...
Replies
Comment: Same methylation probe ID with different locus annotations in Illumina 27k and 4
by
yuabrahamliu
• 0
Thank you for the reply Kevin. I further checked the sequences of the probes and found something noteworthy. For the 27k package, the seque…
Comment: problem installing ENmix package
by
James W. MacDonald
56k
Will you give the full output that you get when installing?
Comment: problem installing ENmix package
by
lea
• 0
I tried both (with the slashes the other way around), it did not work but I delete the package directly on my file browser and it correctly…
Comment: problem installing ENmix package
by
James W. MacDonald
56k
Ugh. You need to convert the back slashes in the call to `unlink` to forward slashes or R will get all huffy with you.
Comment: problem installing ENmix package
by
James W. MacDonald
56k
Ah, that explains it. When R installs a package, it first creates a directory in your library dir called 00LOCK and does a preliminary inst…
Votes
Comment: DMRcate extractRanges error
Comment: Does hashedDrops support 'imbalanced' combinations of HTOs?
SBGNview: Data Analysis, Integration and Visualization on 5000+ Pathways/3000+ Species
A: Minfi issue: return code from pthread_create() is 22
Answer: DiffBind fragmentSize meaning
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