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questions
2
votes
2
replies
961
views
How to obtain low mappability regions from UCSC for deepTools computeGCBias?
deepTools
updated 16 months ago by
GenoMax
146k • written 16 months ago by
chiefcat
▴ 180
46
votes
4
replies
31k
views
ChIP-seq analysis: Tutorial for Beginners
ChIP-Seq
Dummy
updated 3.8 years ago by
ATpoint
84k • written 7.1 years ago by
chiefcat
▴ 180
5
votes
7
replies
3.1k
views
[ChIP-seq. signal plot] How to align the based line of different samples?
deepTools
ChIP-seq
normalization
updated 5.1 years ago by
rls_08
▴ 40 • written 6.8 years ago by
chiefcat
▴ 180
0
votes
2
replies
2.6k
views
Any database for downloading cancer cell-lines transcriptome differential expressed gene (DEG) list? (Normal vs cancer cell-lines)
RNA-Seq
DEG
database
cancer
microarray
updated 5.7 years ago by
Joseph Hughes
★ 3.0k • written 5.7 years ago by
chiefcat
▴ 180
0
votes
0
replies
1.8k
views
Homer [findMotifsGenome.pl] result interputation.
ChIP-Seq
Homer
motif
6.5 years ago by
chiefcat
▴ 180
0
votes
0
replies
1.2k
views
Infer protein function by Gene ontology (ChIP-seq. dataset)
ChIP-Seq
Gene ontology
6.6 years ago by
chiefcat
▴ 180
0
votes
1
reply
1.8k
views
Are there any tools which can plot biclustered heatmap on ChIP-seq. signal?
ChIP-Seq
heatmap
clustering
6.7 years ago by
chiefcat
▴ 180
2
votes
3
replies
3.8k
views
[ChIP-seq. signal plot] How to merge ChIP-seq. biological replicates for signal profile plotting?
deepTools
ChIP-Seq
biological replicates
updated 6.8 years ago by
Devon Ryan
104k • written 6.8 years ago by
chiefcat
▴ 180
1
vote
1
reply
4.9k
views
Input control for ChIP-seq. [Seeking for the clarification between "Library DNA conc.", "no. of raw reads", and "normalization"]
ChIP-Seq
normalization
sample preperation
updated 6.8 years ago by
Carlo Yague
8.8k • written 6.8 years ago by
chiefcat
▴ 180
1
vote
2
replies
3.9k
views
[ChIPSeeker] Getting overlapping genomic feature annotation (e.g. peak locate in gene A & defined TSS region of gene B)
ChIPseeker
annotation
ChIP-Seq
updated 7.0 years ago by
Guangchuang Yu
★ 2.6k • written 7.0 years ago by
chiefcat
▴ 180
8
votes
4
replies
4.0k
views
[How to Save plots in R] DiffBind
ChIP-Seq
R
DiffBind
updated 7.0 years ago by
Rory Stark
★ 2.1k • written 7.0 years ago by
chiefcat
▴ 180
4
votes
4
replies
1.8k
views
Signal desert in ChIP-seq. data? (no signal/ noise in some regions)
ChIP-Seq
updated 7.0 years ago by
Carlo Yague
8.8k • written 7.0 years ago by
chiefcat
▴ 180
1
vote
2
replies
1.7k
views
Gene annotation from genomic features
ChIP-Seq
RNA-Seq
Annotation
7.0 years ago by
chiefcat
▴ 180
3
votes
1
reply
1.7k
views
[Graph plotting] Correlation between gene expression & histone marks (Anyone know how to plot one/ the one like this figure?)
RNA-Seq
ChIP-Seq
updated 7.1 years ago by
Jean-Karim Heriche
27k • written 7.1 years ago by
chiefcat
▴ 180
1
vote
8
replies
2.3k
views
Tools for investigating the correlation of differential gene expression & histone marks/ TF binding?
RNA-Seq
ChIP-Seq
Integration
updated 7.1 years ago by
amy.bashir
▴ 110 • written 7.1 years ago by
chiefcat
▴ 180
1
vote
2
replies
5.8k
views
Homer motif analysis: "Very close % of target vs % of Background sequences with Motif" & "SeqBias at 1st rank"
ChIP-Seq
Homer
Motif
updated 14 months ago by
os306
▴ 10 • written 7.1 years ago by
chiefcat
▴ 180
1
vote
9
replies
5.2k
views
ChIP-seq differential peak calling (Any way to set the window size for calling differential enriched peaks?)
ChIP-Seq
Differential peak calling
MACS2
bdgdiff
7.1 years ago by
chiefcat
▴ 180
0
votes
1
reply
4.6k
views
Appropriate peak length of ChIP-seq. (Histone modification having different pattern at gene body & promoter & intergenic regions)
ChIP-Seq
Peak length
Histone modification
updated 7.1 years ago by
GouthamAtla
12k • written 7.1 years ago by
chiefcat
▴ 180
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