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Chipseq
•
reset
5
votes
6
replies
6.7k
views
Analyzing data without replicates using DiffBind
diffbind
bioconductor
differential binding analysis
without replicate
chipseq
8.2 years ago
Hesh
▴ 10
0
votes
1
reply
3.1k
views
how to define the downstream range in ChIPseeker
ChIPseeker
H3K27me3
chipseq
chipseeker
updated 8.2 years ago by
Guangchuang Yu
★ 1.2k • written 8.2 years ago by
lifeng.liu.biology
▴ 10
2
votes
2
replies
1.1k
views
Cleaning up DiffBind counts in relation to chromosome map
diffbind
chipseq
differential binding analysis
updated 8.2 years ago by
Rory Stark
★ 5.3k • written 8.2 years ago by
rbronste
▴ 60
0
votes
0
replies
1.4k
views
Removing/combining specific annotation categories in ChIPSeeker plots/analysis
chipseeker
chipseq
annotation
8.2 years ago
rbronste
▴ 60
2
votes
3
replies
3.7k
views
ChIPseeker peak annotation tssRegion
chipseeker
annotation
chipseq
8.2 years ago
lifeng.liu.biology
▴ 10
3
votes
7
replies
3.2k
views
complex design for chip-seq analysis
chipseq
csaw
limma
design matrix
multiple factor design
updated 8.3 years ago by
Aaron Lun
★ 29k • written 8.3 years ago by
Assa Yeroslaviz
★ 1.5k
0
votes
1
reply
1.6k
views
Pseudo-coloring DiffBind volcano plot
diffbind
chipseq
volcanoplot
ggplot2
updated 8.3 years ago by
Rory Stark
★ 5.3k • written 8.3 years ago by
rbronste
▴ 60
1
vote
3
replies
2.7k
views
DiffBind error: diffbind DESeq2 analysis has not been run for this contrast
DiffBind
R
chipseq
updated 2.1 years ago by
Rory Stark
★ 5.3k • written 8.4 years ago by
kyliecode
• 0
0
votes
0
replies
1.6k
views
Assigning stats to differential peak locations relative to TSS
chipseeker
chipseq
statistics
8.4 years ago
rbronste
▴ 60
2
votes
1
reply
3.8k
views
ChIPseeker mapping between keys and columns
chipseeker
chipseq
updated 8.4 years ago by
Gavin Kelly
▴ 690 • written 8.4 years ago by
rbronste
▴ 60
1
vote
1
reply
3.4k
views
DiffBind broad and narrow peak identification
diffbind
r
chipseq
updated 8.4 years ago by
Rory Stark
★ 5.3k • written 8.4 years ago by
reubenmcgregor88
• 0
2
votes
3
replies
2.9k
views
MA plot DiffBind in ggplot2
diffbind
ggplot2
r
chipseq
updated 8.4 years ago by
Rory Stark
★ 5.3k • written 8.4 years ago by
reubenmcgregor88
• 0
1
vote
1
reply
1.2k
views
Diffbind Consensus vs Differential peak sets from same count
diffbind
chipseq
updated 8.4 years ago by
Rory Stark
★ 5.3k • written 8.4 years ago by
rbronste
▴ 60
0
votes
0
replies
1.4k
views
Plotting DataTrack for non-model organism.
Gviz
plot
chipseq
8.4 years ago
anupriyaverma1408
• 0
2
votes
10
replies
3.0k
views
DiffBind consensus peak help
diffbind
r
chipseq
updated 8.4 years ago by
Rory Stark
★ 5.3k • written 8.4 years ago by
reubenmcgregor88
• 0
1
vote
2
replies
1.3k
views
DiffBind masks for counts
diffbind
chipseq
updated 8.4 years ago by
Rory Stark
★ 5.3k • written 8.5 years ago by
rbronste
▴ 60
2
votes
2
replies
1.9k
views
DiffBind contrasts issue
diffbind
chipseq
updated 8.4 years ago by
Rory Stark
★ 5.3k • written 8.5 years ago by
rbronste
▴ 60
5
votes
4
replies
2.9k
views
Modeling input data in ChIP-seq experiments with EdgeR, DESeq(2) or Limma
edgeR
deseq2
chipseq
limma
updated 8.6 years ago by
Aaron Lun
★ 29k • written 8.6 years ago by
k.vitting.seerup
▴ 120
27
votes
22
replies
23k
views
DESeq2 for ChIP-seq differential peaks
deseq2
deseq
chipseq
updated 8.6 years ago by
k.vitting.seerup
▴ 120 • written 10.4 years ago by
tangming2005
▴ 200
0
votes
2
replies
1.1k
views
How to set the amount of RAM used for Package 'BCRANK' ?
chipseq
BCRANK
updated 8.6 years ago by
James W. MacDonald
68k • written 8.6 years ago by
rezapanahi222
• 0
0
votes
0
replies
1.1k
views
tools or package for meta-analysis of chip-seq result
chipseq
meta-analysis
8.7 years ago
rezapanahi222
• 0
2
votes
4
replies
2.2k
views
R package for Meta-Analysis of CHIP-Seq data
chipseq
meta-analysis
ubuntu
8.7 years ago
rezapanahi222
• 0
1
vote
7
replies
3.5k
views
loading dba.plotVolcano in DiffBind
diffbind
chipseq
atac-seq
rory stark
updated 8.8 years ago by
Rory Stark
★ 5.3k • written 8.8 years ago by
andrew.gehrke
• 0
2
votes
4
replies
4.3k
views
Error in DESeqDataSetFromHTSeqCount: Gene IDs (first column) differ between files.
chipseq
deseq2
htseqcounts
updated 2.9 years ago by
mhashan.j
▴ 10 • written 9.0 years ago by
JunLVI
▴ 40
3
votes
6
replies
2.6k
views
Differential Pol2 pausing analysis
edger
csaw
chipseq
differential binding analysis
updated 9.0 years ago by
Aaron Lun
★ 29k • written 9.0 years ago by
dalerr
• 0
3
votes
3
replies
2.2k
views
Use csaw to build matrix for heatmap?
csaw
chipseq
edger
updated 9.0 years ago by
Aaron Lun
★ 29k • written 9.0 years ago by
jmKeith
• 0
0
votes
2
replies
2.2k
views
How to take sample peak from each chromosome in peak bed files ?
r
chipseq
encode
peak
9.2 years ago
Jurat Shahidin
▴ 80
0
votes
0
replies
982
views
ChIPseeker result of covplot all over the place
chipseq
9.2 years ago
Stane
▴ 40
1
vote
2
replies
1.4k
views
Providing specific regions to Diffbind
diffbind
chipseq
updated 9.3 years ago by
Rory Stark
★ 5.3k • written 9.3 years ago by
sergio.espeso-gil
• 0
1
vote
3
replies
1.9k
views
DiffBind Error when dba.count on a pre-defined peak set
diffbind
chipseq
updated 9.3 years ago by
Rory Stark
★ 5.3k • written 9.3 years ago by
tangming2005
▴ 200
0
votes
1
reply
1.3k
views
Gviz error after updating R
software error
Gviz
chipseq
rnaseq
9.4 years ago
ta_awwad
▴ 10
1
vote
2
replies
1.8k
views
question regarding custom normalizationFactors in DESeq2
deseq2
R
chipseq
normalization
updated 9.4 years ago by
Simon Anders
★ 3.8k • written 9.4 years ago by
walter.eckalbar
• 0
3
votes
2
replies
3.1k
views
DiffBind "no lines available in input" error
diffbind
chipseq
updated 9.6 years ago by
Rory Stark
★ 5.3k • written 9.6 years ago by
igor
▴ 50
0
votes
1
reply
2.5k
views
DiffBind TMM normalization
Rory Stark
diffbind
TMM
edgeR
chipseq
updated 9.6 years ago by
Rory Stark
★ 5.3k • written 9.8 years ago by
akdess
• 0
0
votes
1
reply
1.6k
views
DiffBind: Consensus peak score ?
diffbind
peak
chipseq
updated 9.6 years ago by
Rory Stark
★ 5.3k • written 9.6 years ago by
becavin.christophe
• 0
1
vote
0
replies
2.5k
views
Job:
Bioinformatics Scientist @ Berlin Institute for Medical Systems Biology
rnaseq
snp
chipseq
Job
9.7 years ago
altuna akalin
▴ 20
2
votes
2
replies
2.7k
views
Can I calculate counts from the base mean and log2fc outputs of DESeq2? Also, can I calculate error for counts values from lfcse output?
deseq2
chipseq
counts
log2fc
error
updated 9.7 years ago by
Michael Love
43k • written 9.7 years ago by
robin.uchiyama
• 0
0
votes
1
reply
1.2k
views
error in noGGi
software error
seqnames
characters
r
chipseq
9.7 years ago
awakumaya
• 0
4
votes
1
reply
3.7k
views
csaw - workflow to incorporate input/control samples?
csaw
chipseq
differential binding analysis
updated 9.8 years ago by
Aaron Lun
★ 29k • written 9.8 years ago by
markus.ringner
▴ 10
0
votes
1
reply
1.8k
views
ChipQCSample error Error in `colnames<-`(`*tmp*`, value = c("A", "B", "C")) : length of 'dimnames' [2] not equal to array extent
chipseq
chipqc
updated 9.8 years ago by
Thomas Carroll
▴ 420 • written 9.8 years ago by
ssn4ssn
• 0
1
vote
1
reply
2.0k
views
Differential binding using csaw
csaw
differential binding analysis
chipseq
differential expression
differential gene expression
updated 9.8 years ago by
Aaron Lun
★ 29k • written 9.8 years ago by
Amitha Sampath
▴ 10
0
votes
0
replies
1.3k
views
Error in makeCountSet function in ChIPComp package
ChIPSeq
ChIPComp
makeCountSet
10.0 years ago
AB
▴ 110
1
vote
1
reply
2.9k
views
Generating unexpected peaks from DiffBind
diffbind
chipseq
updated 10.1 years ago by
Rory Stark
★ 5.3k • written 10.1 years ago by
michael.alexander.finger
• 0
0
votes
5
replies
2.3k
views
CSAW: Error: could not find function "normOffsets"
csaw
edgeR
chipseq
updated 10.1 years ago by
Aaron Lun
★ 29k • written 10.1 years ago by
gthm
▴ 30
1
vote
1
reply
2.5k
views
ChIP-seq, peak annotation using ChIPpeakAnno
chipseq
chippeakanno
updated 10.2 years ago by
Ou, Jianhong
★ 1.3k • written 10.2 years ago by
michaelR
• 0
0
votes
0
replies
2.4k
views
Job:
Bioinformatics Data Analyst - IMP/IMBA Vienna
chipseq
atac-seq
gro-seq
bsseq
rnaseq
Job
10.3 years ago
Jaritz,Markus
▴ 20
0
votes
3
replies
2.2k
views
Error in ChIPQC
chipseq
ChIPQ
updated 10.3 years ago by
Valerie Obenchain
★ 6.8k • written 10.4 years ago by
lindahove
▴ 10
1
vote
4
replies
3.1k
views
ChIPseeker: Is it possible to create heatmaps / metagene plots without being centered on the TSS?
chipseq
chipseeker
exon start site
updated 10.3 years ago by
Guangchuang Yu
★ 1.2k • written 10.3 years ago by
cguzman.roma
• 0
0
votes
0
replies
1.5k
views
p value for correlation of two bed files
chipseq
10.3 years ago
Gyan Prakash Mishra
▴ 10
7
votes
11
replies
6.6k
views
annotatePeak() in ChIPseeker - how long does it take to run?
annotatePeak
chipseeker
chipseq
org.Mm.eg.db
TxDb.Mmusculus.UCSC.mm9.knownGene
updated 10.3 years ago by
Martin Morgan
25k • written 10.5 years ago by
Elsa
• 0
195 results • Page
3 of 4
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Replies
Comment: soGGi error
by
shepherl
4.3k
We have tried to contact the soGGi maintainer to have them update the package to the newer version of gglot2 but they have so far been unre…
Comment: using limma trend workflow in CAMERA
by
Gordon Smyth
53k
No, `trend.var=TRUE` and `trend=TRUE` are not needed in any voom pipeline, because the trend is already incorporated into the voom weights.
Comment: Questions about bacon QC and correction on EWAS results
by
Tikaaa2sahaaaq2c
• 0
In the world of mobile games, the 88ef game download has gained traction for its performance driven design [free download][1], similar to …
Comment: using limma trend workflow in CAMERA
by
A.Barden
▴ 20
Do you need to set trend.var=TRUE when using camera in the limma-voom pipeline with RNA-Seq data (as apposed to limma-trend pipeline)?
Comment: Upcoming Ensembl API and data access changes - new blog post available
by
Tikaaa2sahaaaq2c
• 0
Just as the Ensembl team transitions to a new platform for streamlined data access, diners can benefit from a digital newks menu prices con…
Votes
Answer: DiffBind differential analysis
Answer: Limma-voom sample weights and impact on DEG numbers
C: Why limma, edgeR, and DESeq did not implement fold change moderation first?
Comment: using limma trend workflow in CAMERA
C: z-score with DESeq2?
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