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Showing top results for tag:
Peak
•
reset
0
votes
0
replies
96
views
HOMER findPeaks: what does -fdr actually do?
homer
atac-seq
calling
peak
dap-seq
chip-seq
14 days ago by
mcsimenc
▴ 20
2
votes
5
replies
474
views
How to View Peaks from ChIP-seq Data generated using old reference genome (hg18)
R
Peak
ChIP-seq
updated 9 weeks ago by
ATpoint
85k • written 9 weeks ago by
DareDevil
★ 4.3k
0
votes
0
replies
242
views
cross-correlation peak at position 0 when calculating ChIp-Seq
cross-correlation
peak
chip-seq
phantompeak
ChIPseeker
9 months ago by
Assa Yeroslaviz
★ 1.9k
0
votes
0
replies
363
views
ChIPseq gapped and braod peaks file are empty
ChIPseq
broadpeak
gapped
peak
12 months ago by
Mehvi khan
• 0
3
votes
1
reply
613
views
Extremely high ChIP-seq peak at mouse Chr2 "Gm10800" region
ChIPseq
peak
TF
chipseq
updated 14 months ago by
ATpoint
85k • written 14 months ago by
Ri
▴ 30
0
votes
0
replies
566
views
Annotation of ATAC-seq peak - distal intergenic regions as enhancers
annotation
peak
ATAC-seq
15 months ago by
Pei
▴ 220
0
votes
1
reply
699
views
how to look at interacting SNP for a gene using Hic contact map
peak
interaction
contact-map
Hi-C
updated 18 months ago by
james.hawley
▴ 70 • written 18 months ago by
rheab1230
▴ 140
0
votes
0
replies
421
views
Does the bigwig file of a single-end chip-seq shows 2 peaks for a fragment whereas the paired-end show one peak ?
peak
chip-seq
bigwig
single-end
updated 19 months ago by
Ram
44k • written 19 months ago by
Rajendra KC
▴ 20
0
votes
0
replies
627
views
Differential Peak Analysis for a specific gene using only bigWig + BED files?
differential
peak
bigwig
chip-seq
analysis
21 months ago by
Maycon
• 0
3
votes
2
replies
556
views
Peak Calling on a single gene?
chip
peak
illumina
calling
chip-seq
updated 21 months ago by
ATpoint
85k • written 21 months ago by
Maycon
• 0
2
votes
2
replies
856
views
Quantifying Peak Height Difference in ATAC-seq
differential
peak
ATAC-seq
calling
analysis
24 months ago by
jjstevens
• 0
0
votes
0
replies
831
views
MACS2 not working in paired end mode
NGS
bowtie2
macs2
peak
calling
24 months ago by
Filago
▴ 100
0
votes
3
replies
858
views
MACS2 sample grouping
peak
calling
MACS2
updated 2.0 years ago by
ATpoint
85k • written 2.0 years ago by
Beth
▴ 10
0
votes
2
replies
850
views
Find overlaps within a GRanges object
Peak
Overlap
GRanges
IRanges
R
2.0 years ago by
yangliu326459
▴ 30
0
votes
1
reply
496
views
Microsatellite analysis Peak height data
microsatellite
peak
height
forensic
fsa
updated 2.0 years ago by
Jesse
▴ 850 • written 2.1 years ago by
genomics_buddy
• 0
0
votes
1
reply
584
views
identification of overlapped, proximal and distal gene for peak regions
chip
idenfication
peak
seq
gene
updated 2.1 years ago by
husensofteng
▴ 410 • written 2.1 years ago by
Omics data mining
▴ 260
0
votes
0
replies
334
views
how to know about peak expression of gene
peak
expression
2.3 years ago by
aimanbarki
▴ 20
4
votes
0
replies
927
views
how could I select low 'fraction fragments overlapping peaks' but 'high fragments per barcode' in scATAC-seq analysis?
cellranger
ATAC-seq
peak
ATAC
10x
2.4 years ago by
Chilly
★ 1.3k
0
votes
1
reply
589
views
how to use custom genome i.e. E. Coli in epic2 ?
coli
peak
epigenomics
calling
epic2
updated 2.5 years ago by
Carlo Yague
8.9k • written 2.5 years ago by
Ankana
• 0
2
votes
4
replies
1.7k
views
Why the bed file not recognized as a bed file
peak
bed
updated 19 months ago by
Ram
44k • written 2.5 years ago by
brgs
• 0
3
votes
3
replies
2.1k
views
ATAC DiffBind: use peak or summit file?
peak
ATAC-seq
bed
diffbind
summit
2.6 years ago by
a_bis
▴ 40
5
votes
4
replies
4.3k
views
why are all DiffBind tutorial's ATAC-seq peak intervals 400 bp for all intervals?
peak
ATAC-seq
intervals
DiffBind
consensus
updated 2.9 years ago by
Rory Stark
★ 2.1k • written 3.0 years ago by
mrj
▴ 180
7
votes
7
replies
2.9k
views
How to merge samples of the same cell type to do differential peak calling?
ATAC-seq
calling
merge
differential
peak
updated 2.9 years ago by
R_newbie
• 0 • written 2.9 years ago by
zau saa
▴ 150
0
votes
0
replies
839
views
Comparison of ChIPseeker and GREAT peak annotations
Peak
annotation
GREAT
ChIPseeker
3.0 years ago by
MS
▴ 40
0
votes
0
replies
554
views
What's the biology meaning of multi-peak in a region
peak
ATAC
3.2 years ago by
shangguandong1996
▴ 30
1
vote
3
replies
1.6k
views
Can I use All Peaks (MACS2 -q 1) for analysis?
Peak
DiffBind
MACS2
3.3 years ago by
Tian
▴ 50
1
vote
4
replies
2.1k
views
How to plot chipseq peak relative to TSS for some genes ?
chipseq
R
plotwithR
TSS
peak
updated 3.5 years ago by
Carambakaracho
★ 3.3k • written 3.5 years ago by
Sarah
▴ 10
3
votes
3
replies
2.9k
views
New to ATAC-seq single cell
atac-seq
peak
updated 3.5 years ago by
Friederike
9.0k • written 3.5 years ago by
zizigolu
★ 4.3k
0
votes
1
reply
2.1k
views
how to run and use the ENCODE ATAC-seq pipline
ATAC-seq
ENCODE
peak
updated 3.5 years ago by
Jeremy Leipzig
22k • written 3.7 years ago by
cwwong13
▴ 40
0
votes
1
reply
1.4k
views
Determine the significance of peak overlaps (bedtools)
bedtools
peak
ChIP-seq
eCLIP
updated 3.6 years ago by
Istvan Albert
101k • written 3.6 years ago by
kstangline
▴ 80
3
votes
2
replies
1.1k
views
how to calculate distance from a single nucleotide position to a peak
ChIP-Seq
peak
distance
genome
updated 3.9 years ago by
Alex Reynolds
35k • written 3.9 years ago by
Lila M
★ 1.3k
17
votes
2
replies
13k
views
Finding overlaps between GRanges objects
GRanges
promoter
peak
IRanges
ChIP-Seq
updated 4.0 years ago by
Jimbou
▴ 950 • written 4.0 years ago by
mickey_95
▴ 110
0
votes
0
replies
1.3k
views
eCLIP-seq peak calling using HOMER
RNA-Seq
CLIP-Seq
HOMER
Peak
Algorithm
4.3 years ago by
dahun73
▴ 10
1
vote
2
replies
1.5k
views
Retrieve coordinate for maximum value in a region using a bigwig file
bigwig
peak
summit
updated 4.5 years ago by
Pierre Lindenbaum
164k • written 4.5 years ago by
am2622
• 0
0
votes
0
replies
846
views
MeDIP seq data analysis
medip
peak calling
aligment
peak
methylation
updated 4.6 years ago by
GenoMax
146k • written 4.6 years ago by
iridha
• 0
6
votes
6
replies
6.2k
views
7 follow
RIP-Seq data analysis
RNA-Seq
IP
sequencing
Peak
updated 2.9 years ago by
GiV17
▴ 50 • written 5.7 years ago by
flyguymail22
▴ 10
0
votes
1
reply
1.4k
views
How to annotate peaks without strand information
peak
homer
updated 5.0 years ago by
Biostar
20 • written 5.1 years ago by
ashafik
• 0
0
votes
0
replies
2.3k
views
Different parameters for macs2 to call narrow marks and broad marks?
ChIP-Seq
macs2
histone modification
peak
5.5 years ago by
ben.kunfang
▴ 30
0
votes
0
replies
1.0k
views
how to deal with H3K4me3 and H3K4me1 overlap peaks?
ChIP-Seq
macs2
peak
histone modification
5.5 years ago by
ben.kunfang
▴ 30
0
votes
1
reply
975
views
H3K27ac peaks identification from UCSC hg19 annotation database
H3K27ac
peak
input
5.7 years ago by
Shicheng Guo
★ 9.5k
12
votes
3
replies
24k
views
bigwig to peak
peak
bigwig
chip-seq
updated 3.0 years ago by
Ram
44k • written 10.3 years ago by
Nicolas Rosewick
11k
0
votes
2
replies
3.1k
views
mm10 enhancer annotation for ngs.plot.r
ChIP-Seq
peak
visualization
updated 6.3 years ago by
whm568019240
• 0 • written 7.6 years ago by
m.sadman.sakib
▴ 120
0
votes
1
reply
1.4k
views
What can overlapping peaks in ChIP-seq samples tell?
ChIP-Seq
Peak
Overlapping
Repeated evidence
updated 6.5 years ago by
goodez
▴ 640 • written 6.5 years ago by
bwd
▴ 90
1
vote
5
replies
3.2k
views
How to extrach gene names and peaks from BedGraph or BigWig files
ChIP-Seq
bedgraph
bigwig
peak
updated 6.5 years ago by
Devon Ryan
104k • written 6.5 years ago by
hkarakurt
▴ 180
1
vote
4
replies
1.7k
views
occupancy at common specific TF binding sites
ChIP-Seq
R
peak
density
bins
updated 6.9 years ago by
Kevin Blighe
88k • written 6.9 years ago by
woongjaej
▴ 30
10
votes
7
replies
4.1k
views
Chip-seq peak annotation [Chipseeker]
ChIP-Seq
chipseeker
peak
annotation
updated 7.4 years ago by
Guangchuang Yu
★ 2.6k • written 7.4 years ago by
anu014
▴ 190
3
votes
2
replies
1.6k
views
How to make conditional duplicate removal for list of peak file?
r
ChIP-Seq
sequencing
peak
updated 7.8 years ago by
Alex Reynolds
35k • written 7.8 years ago by
Jurat Shahidin
▴ 100
6
votes
11
replies
2.7k
views
How to edit large bed files in order to keep peaks in particular chromosome ?
R
ChIP-Seq
genome
peak
encode
updated 7.9 years ago by
Alex Reynolds
35k • written 7.9 years ago by
Jurat Shahidin
▴ 100
10
votes
6
replies
2.6k
views
Any way to merge peak overlap hit table more efficiently ?
R
peak
iranges
sequencing
ChIP-Seq
8.0 years ago by
Jurat Shahidin
▴ 100
2
votes
4
replies
2.8k
views
how to split "blocks" in one entry of bed file into different entries
bed format
peak
updated 8.0 years ago by
Alex Reynolds
35k • written 8.0 years ago by
scottzijiezhang
• 0
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