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ChIPSeq
•
reset
3
votes
6
replies
4.3k
views
Analyzing data without replicates using DiffBind
diffbind
bioconductor
differential binding analysis
without replicate
chipseq
6.4 years ago • updated 6.3 years ago
Hesh
▴ 10
3
votes
9
replies
2.8k
views
ChIPQC and broadPeak input
chipseq
chipqc
chip-seq
8.6 years ago
lindahove
▴ 10
2
votes
6
replies
2.4k
views
ChIPseeker: covplot function: error with some ENCODE data sets
chiPseeker
covplot
ENCODE
ChIpseq
8.9 years ago
sarabusquets88
• 0
5
votes
5
replies
2.0k
views
Metagenomic analysis: Aligning ChIPseq data on TSS
metagenomics
chipseq
biomart
shortread
convert
biomaRt
9.5 years ago
patrick.schordert
▴ 30
1
vote
4
replies
1.9k
views
MAnorm output as DiffBind input.
MAnorm
diffbind
normalization
chipseq
updated 3.4 years ago by
Rory Stark
★ 5.1k • written 6.2 years ago by
ajeet
• 0
26
votes
22
replies
18k
views
DESeq2 for ChIP-seq differential peaks
deseq2
deseq
chipseq
updated 6.7 years ago by
k.vitting.seerup
▴ 120 • written 8.5 years ago by
tangming2005
▴ 190
8
votes
9
replies
6.0k
views
ChIPseq-style peak calling for paired-end sequencing?
Chipseq
DNAseq
ATAC
bayespeak
narrowpeaks
updated 8.8 years ago by
Gordon Smyth
50k • written 8.9 years ago by
samuel collombet
▴ 140
0
votes
3
replies
1.6k
views
Problem with rGADEM & MotIV - one matrix consensus after GADEM() and one plot enrichment motif
rgadem
motiv
chipseq
jaspar
updated 8.8 years ago by
emercier
• 0 • written 8.9 years ago by
w.jarassier
• 0
3
votes
12
replies
3.2k
views
Is it possible to change how DiffBind merge peaks?
DiffBind
ChIPseq
updated 2.6 years ago by
Rory Stark
★ 5.1k • written 4.5 years ago by
zhenfeng.liu1
▴ 20
7
votes
11
replies
4.7k
views
annotatePeak() in ChIPseeker - how long does it take to run?
annotatePeak
chipseeker
chipseq
org.Mm.eg.db
TxDb.Mmusculus.UCSC.mm9.knownGene
updated 8.5 years ago by
Martin Morgan
25k • written 8.7 years ago by
Elsa
• 0
2
votes
4
replies
1.5k
views
R package for Meta-Analysis of CHIP-Seq data
chipseq
meta-analysis
ubuntu
6.8 years ago
rezapanahi222
• 0
4
votes
3
replies
1.2k
views
Opinions on DESeqDataSetFromMatrix rowSums minimum for ChIP and/or ATAC-seq
deseq2
atac-seq
chipseq
differential binding analysis
updated 6.3 years ago by
Aaron Lun
★ 28k • written 6.3 years ago by
rbronste
▴ 60
0
votes
3
replies
3.9k
views
unknown error in DiffBind package
ChIPSeq
chipseq
DiffBind
ChIPSeq
chipseq
DiffBind
updated 9.9 years ago by
Rory Stark
★ 5.1k • written 10.0 years ago by
Guest User
★ 13k
0
votes
6
replies
1.8k
views
IdeogramTrack and bigWig file errors in Gviz
ChIPSeq
GO
rtracklayer
CAMERA
chipseq
Gviz
ChIPSeq
GO
rtracklayer
CAMERA
chipseq
Gviz
updated 10.9 years ago by
Robert Ivanek
▴ 730 • written 10.9 years ago by
Guest User
★ 13k
0
votes
2
replies
942
views
mypeaklist in ChIPpeakAnno
ChIPSeq
chipseq
ChIPSeq
chipseq
13.6 years ago
Julie Zhu
★ 4.3k
0
votes
6
replies
1.6k
views
cel files with affy library
ChIPSeq
updated 2.6 years ago by
almaza24map
• 0 • written 2.6 years ago by
scipio04
• 0
5
votes
8
replies
932
views
Help with error install csaw
ChIPSeq
ATACSeq
updated 11 months ago by
nekisaf309
• 0 • written 12 months ago by
Chris
• 0
1
vote
3
replies
2.6k
views
Downsampling ChIP-seq BAM files with spike in normalization factor before feeding into Diffbind
diffbind
chipseq
chipqc
updated 3.4 years ago by
Rory Stark
★ 5.1k • written 6.1 years ago by
bioinfouser2
▴ 10
3
votes
7
replies
1.9k
views
dba.count with pre-defined regions
dba.count
dba
chipseq
diffbind
updated 6.3 years ago by
Rory Stark
★ 5.1k • written 6.3 years ago by
sylvia
▴ 10
3
votes
3
replies
4.0k
views
Error "if (is.na(peaks)) { : argument is of length zero " in DiffBind
diffbind
chipseq
peaks
dba
is.na
6.0 years ago • updated 5.9 years ago
maria.kondili
▴ 10
3
votes
4
replies
2.4k
views
ChIPseeker/Question about ''annoatePeak' function and for Bioconductor AnnotationData Packages for L.japonicus
chipseeker
Bioconductor AnnotationData Packages
Lotus japonicus
ChIPseq
updated 5.5 years ago by
James W. MacDonald
65k • written 5.5 years ago by
egbastakis
• 0
2
votes
4
replies
1.7k
views
Integrating the computed spike-in coefficients for the normalisation before differential peaks analysis
DiffBind
Chipseq
spike-ins
updated 3.4 years ago by
Rory Stark
★ 5.1k • written 4.4 years ago by
Konstantin Okonechnikov
▴ 40
5
votes
8
replies
2.1k
views
how to construct a DBA object from count matrix
ChIPSeq
ATACSeq
differentially_occupied
DiffBind
updated 21 months ago by
Johanna Hardin
▴ 20 • written 2.7 years ago by
pegah.taklifi
▴ 30
2
votes
3
replies
2.1k
views
MA plot DiffBind in ggplot2
diffbind
ggplot2
r
chipseq
updated 6.5 years ago by
Rory Stark
★ 5.1k • written 6.6 years ago by
reubenmcgregor88
• 0
0
votes
2
replies
1.4k
views
chip-seq data analysis
Transcription
ChIPSeq
Alignment
chipseq
Transcription
ChIPSeq
Alignment
chipseq
updated 14.1 years ago by
Sean Davis
21k • written 14.1 years ago by
Tiandao Li
▴ 60
0
votes
2
replies
1.4k
views
Extracting overlapping gene names from a list of peaks
ChIPSeq
chipseq
ChIPSeq
chipseq
updated 10.6 years ago by
Michael Lawrence
★ 11k • written 10.6 years ago by
Patrick Schorderet
▴ 20
2
votes
3
replies
2.5k
views
ChIPseeker peak annotation tssRegion
chipseeker
annotation
chipseq
6.4 years ago
lifeng.liu.biology
▴ 10
2
votes
4
replies
3.4k
views
Error in DESeqDataSetFromHTSeqCount: Gene IDs (first column) differ between files.
chipseq
deseq2
htseqcounts
updated 13 months ago by
mhashan.j
▴ 10 • written 7.1 years ago by
JunLVI
▴ 40
0
votes
2
replies
2.0k
views
Diffbind: Peak score normalization
normalization
chipseq
diffbind
9.2 years ago
medinaale
• 0
0
votes
7
replies
1.6k
views
DiffBind fails to derive consensus peaksets
software error
chipseq
diffbind
updated 8.9 years ago by
Gord Brown
▴ 650 • written 8.9 years ago by
Nicolas Delhomme
▴ 320
3
votes
2
replies
2.4k
views
DiffBind "no lines available in input" error
diffbind
chipseq
updated 7.7 years ago by
Rory Stark
★ 5.1k • written 7.7 years ago by
igor
▴ 40
1
vote
7
replies
2.6k
views
loading dba.plotVolcano in DiffBind
diffbind
chipseq
atac-seq
rory stark
updated 7.0 years ago by
Rory Stark
★ 5.1k • written 7.0 years ago by
andrew.gehrke
• 0
6
votes
6
replies
2.9k
views
Score column for DiffBind::dba.peakset
DiffBind
chipseq
updated 9.0 years ago by
Gord Brown
▴ 650 • written 9.0 years ago by
teckpor
• 0
0
votes
5
replies
2.7k
views
diffbind
DiffBind
chipseq
updated 8 months ago by
Rory Stark
★ 5.1k • written 8 months ago by
ANAMIKA
• 0
2
votes
6
replies
1.4k
views
DiffBind for Allele-specific binding analysis
diffbind
chipseq
updated 8.9 years ago by
Rory Stark
★ 5.1k • written 8.9 years ago by
Vivek.b
▴ 100
0
votes
1
reply
1.5k
views
IdeogramTrack and bigWig file errors in Gviz
ChIPSeq
GO
Network
rtracklayer
CAMERA
chipseq
Gviz
ChIPSeq
GO
Network
rtracklayer
Gviz
updated 10.5 years ago by
Michael Lawrence
★ 11k • written 10.5 years ago by
Miles Pufall
▴ 40
0
votes
1
reply
815
views
"islands" and number of reads in the island in package chipseq/ShortRead
ChIPSeq
Coverage
chipseq
ChIPSeq
Coverage
chipseq
updated 14.3 years ago by
Kasper Daniel Hansen
★ 6.5k • written 14.3 years ago by
Nora Rieber
▴ 40
1
vote
3
replies
1.2k
views
DiffBind Error when dba.count on a pre-defined peak set
diffbind
chipseq
updated 7.5 years ago by
Rory Stark
★ 5.1k • written 7.5 years ago by
tangming2005
▴ 190
0
votes
1
reply
3.0k
views
merge error: 'by.x' and 'by.y' specify different numbers of columns
ChIPSeq
biomaRt
chipseq
ChIPSeq
biomaRt
chipseq
updated 9.8 years ago by
James W. MacDonald
65k • written 9.8 years ago by
Tran, Nhu Quynh T
▴ 50
0
votes
2
replies
1.2k
views
ChIPpeakAnno - VennDiagram P-value - NaN
ChIPSeq
chipseq
ChIPpeakAnno
ChIPSeq
chipseq
ChIPpeakAnno
13.6 years ago
Julie Zhu
★ 4.3k
1
vote
2
replies
920
views
Providing specific regions to Diffbind
diffbind
chipseq
updated 7.4 years ago by
Rory Stark
★ 5.1k • written 7.4 years ago by
sergio.espeso-gil
• 0
0
votes
10
replies
1.4k
views
DESeq on CCAT identified chipseq peaks
ChIPSeq
chipseq
DESeq
ChIPSeq
chipseq
DESeq
updated 9.9 years ago by
Rory Stark
★ 5.1k • written 9.9 years ago by
Guest User
★ 13k
0
votes
1
reply
1.1k
views
Involve tag count information in coverage function (IRanges, chipseq package)?
ChIPSeq
Coverage
chipseq
ChIPSeq
Coverage
chipseq
13.6 years ago
Xiaohui Wu
▴ 280
0
votes
1
reply
1.0k
views
How to install chipseq package
ChIPSeq
chipseq
ChIPSeq
chipseq
updated 15.1 years ago by
Patrick Aboyoun
★ 1.6k • written 15.1 years ago by
Yuan Hao
▴ 90
0
votes
3
replies
1.6k
views
Error in ChIPQC
chipseq
ChIPQ
updated 8.5 years ago by
Valerie Obenchain
★ 6.8k • written 8.5 years ago by
lindahove
▴ 10
4
votes
2
replies
1.7k
views
Confusing error when running ChIPQC
chipqc
chipseq
updated 8.5 years ago by
Thomas Carroll
▴ 420 • written 8.5 years ago by
Ryan C. Thompson
★ 7.9k
1
vote
2
replies
1.3k
views
question regarding custom normalizationFactors in DESeq2
deseq2
R
chipseq
normalization
updated 7.5 years ago by
Simon Anders
★ 3.7k • written 7.5 years ago by
walter.eckalbar
• 0
0
votes
1
reply
918
views
Gviz error after updating R
software error
Gviz
chipseq
rnaseq
7.5 years ago
ta_awwad
▴ 10
0
votes
1
reply
1.6k
views
DiffBind loading Problem
Transcription
ChIPSeq
chipseq
DiffBind
Transcription
ChIPSeq
chipseq
DiffBind
10.1 years ago
Rory Stark
★ 5.1k
0
votes
2
replies
1.5k
views
How to take sample peak from each chromosome in peak bed files ?
r
chipseq
encode
peak
7.3 years ago
Jurat Shahidin
▴ 80
50 results • Page
1 of 1
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