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Chipseq
•
reset
0
votes
2
replies
409
views
Problem in Chip-seq data analysis using MACS3
chipseq
MACSdata
updated 8 weeks ago by
ATpoint
★ 4.9k • written 8 weeks ago by
Gaurav
• 0
0
votes
0
replies
876
views
Diffbind Analysis gives error during profile plotting stage. Error in value[[3L]](cond) : profileplyr error: Error: BiocParallel errors 1 remote…
chipseq
profileplyr
DiffBind
3 months ago
Muhammad
• 0
0
votes
0
replies
280
views
I want my overlapping peaks to stop merging by default doing read counting (using DiffBind in R-studio)
peakoverlap
mergingpeaks
ChIPseq
DiffBind
4 months ago
atlanta
• 0
0
votes
0
replies
246
views
News:
Introduction to Epigenomics data analysis with R and Bioconductor course (online) - 14th-18th April
chipseq
MNaseSeq
ATACSeq
4 months ago
info
▴ 10
1
vote
8
replies
2.5k
views
[ChIP-seq] DESeq2 on counts matrix from union set of called peaks
csaw
ChIPseq
DESeq2
DiffBind
5 months ago • updated 4 months ago
Luca
• 0
1
vote
3
replies
955
views
Csaw normalization strategies - general inquiry
ChIPSeq
csaw
updated 6 months ago by
franknappi14
• 0 • written 6 months ago by
Luca
• 0
6
votes
5
replies
2.1k
views
MEDIPS for chIP-Seq
ChIPSeq
written 3.0 years ago by
Darek
▴ 30
0
votes
0
replies
283
views
ChIP peaks comparison
ChIPSeqData
genomes
ChIPSeq
9 months ago
user_bioinfo
• 0
0
votes
0
replies
423
views
Trying to understand basic DiffBind usage
ChIPSeq
DiffBind
11 months ago
Alejandro
• 0
0
votes
0
replies
631
views
Blacklist regions on DBA object (diffbind)
DiffBind
chipseq
14 months ago
gamma.jian
▴ 10
0
votes
0
replies
642
views
DiffBind: no peaks in DBA object
DiffBind
macs2
chipseq
15 months ago
yvonneh
• 0
0
votes
1
reply
503
views
what is the sampleFiles
chipseq
updated 16 months ago by
James W. MacDonald
68k • written 16 months ago by
zhulin
• 0
0
votes
0
replies
737
views
Best method for annotating distal peaks
ChIPSeq
annotation
ChIPpeakAnno
18 months ago
nilanjanamani88
• 0
1
vote
3
replies
1.0k
views
Big differences between biological replicates makes DESeq2 result 0
chipseq
DifferentialMethylation
DESeq2
updated 18 months ago by
Michael Love
43k • written 19 months ago by
rebw25
• 0
0
votes
0
replies
530
views
Parameter bSubControl with no effect in DiffBind dba.count?
bSubControl
ChIPSeq
DiffBind
19 months ago
frueher
• 0
0
votes
0
replies
879
views
Calculation of ChIP-seq normalization factors with non-conventional spike-in assumptions
csaw
ChIPseq
DiffBind
21 months ago
jared.andrews07
▴ 30
1
vote
1
reply
1.1k
views
DiffBind - how to prep the sample matrix when multiple bam files are used by MACS2's -t and -c param?
DiffBind
chipseq
updated 23 months ago by
James W. MacDonald
68k • written 23 months ago by
lin.pei26
• 0
0
votes
0
replies
666
views
Why there are two pfms in the result of oligoSummary function of ChIPpeakAnno package?
ChIPpeakAnno
ChIPSeq
MotifDiscovery
23 months ago
franciscrick41
• 0
2
votes
14
replies
2.3k
views
ChIPpeakAnno: S.lycopersicum annotation missing
ChIPpeakAnno
ChIPSeq
updated 24 months ago by
James W. MacDonald
68k • written 24 months ago by
Jerina
▴ 10
0
votes
5
replies
7.3k
views
diffbind
DiffBind
chipseq
updated 2.1 years ago by
Rory Stark
★ 5.2k • written 2.1 years ago by
ANAMIKA
• 0
1
vote
4
replies
2.1k
views
DiffBind - Retrieving the differentially bound sites - HOW to calculate fold-change
ChIPSeq
DiffBind
updated 2.2 years ago by
Rory Stark
★ 5.2k • written 2.2 years ago by
lin.pei26
• 0
0
votes
2
replies
1.2k
views
annotate peaks using a custom genome
ChIPSeq
annotate
ChIPpeakAnno
updated 2.3 years ago by
Kai Hu
▴ 70 • written 2.3 years ago by
C T
▴ 140
5
votes
8
replies
1.7k
views
Help with error install csaw
ChIPSeq
ATACSeq
written 2.4 years ago by
Chris
▴ 20
0
votes
2
replies
2.0k
views
DiffBind with ChIPseq from histone analysis: EdgeR or Deseq2?
DESeq2
ChIPSeq
DiffBind
edgeR
HistoneModification
2.4 years ago
Giulia
• 0
0
votes
0
replies
760
views
DiffBind with ChIPseq from histone analysis: EdgeR or Deseq2?
DESeq2
ChIPSeq
DiffBind
edgeR
HistoneModification
2.4 years ago
Giulia
• 0
1
vote
2
replies
1.7k
views
how i can get the name of genes in pathway?
chipseq
ChIPseeker
2.5 years ago
chavaleab
• 0
1
vote
3
replies
1.3k
views
Only getting 10 peaks from mac2 callpeak
ChIPSeq
2.5 years ago
stacy.genovese
• 0
1
vote
4
replies
2.3k
views
How to search a .narrowPeak file for a list of specific genes using GenomicRanges package
ChIPSeq
PeakDetection
2.6 years ago
stacy.genovese
• 0
0
votes
2
replies
1.3k
views
New to ChipSeq getting 0 peaks using dba()
ChipSeq
ChIPSeqData
chipseqDB
2.7 years ago
stacy.genovese
• 0
0
votes
1
reply
1.3k
views
DiffBind question _ SampleSheet / Venn diagram issue
chipseq
DiffBind
updated 2.9 years ago by
Rory Stark
★ 5.2k • written 2.9 years ago by
Nicole
• 0
0
votes
7
replies
2.7k
views
CHIPQC error regarding BiocParallel
CHIPQC
Diffbind
chipseq
rory stark
Thomas Carroll
updated 3.0 years ago by
arisarkar88
▴ 40 • written 5.3 years ago by
bioinfouser2
▴ 10
0
votes
1
reply
1.3k
views
Job:
'Omics data analyst for HPCBio, University of Illinois
Metagenomics
GenomicVariation
Genomics
RNASeq
ChIPSeq
3.1 years ago • updated 3.0 years ago
Jenny Drnevich
★ 2.0k
0
votes
0
replies
1.2k
views
intron coordination and annotation
ChIPSeq
updated 3.1 years ago by
ATpoint
★ 4.9k • written 3.1 years ago by
mehdi
• 0
0
votes
0
replies
1.2k
views
Job:
Bioinformatics Research Scientist- Epigenetics Group
HiC
Epigenetics
HiCHIP
ChIPSeq
3.2 years ago
xubeisi
• 0
0
votes
1
reply
1.0k
views
AssignChromosomeRegion not working in Rstudio 4.2
ChIPpeakAnno
ChIPSeq
updated 3.3 years ago by
Ou, Jianhong
★ 1.3k • written 3.3 years ago by
Abhilansh
• 0
0
votes
3
replies
1.6k
views
DiffBind on static peak set for all samples
ChIPSeq
DiffBind
updated 3.3 years ago by
Rory Stark
★ 5.2k • written 3.3 years ago by
Drew
• 0
0
votes
0
replies
1.0k
views
Can we get an Average Profile of ChIP peaks binding to Transcription "START and STOP site" both in a single plot?
ChIPSeq
ChIPseeker
3.3 years ago
Swadha
• 0
0
votes
2
replies
1.5k
views
Input peak set for DiffBind should be all peaks or FDR filtered?
ChIPSeq
DiffBind
written 3.4 years ago by
rita.rebollo
• 0
1
vote
2
replies
2.1k
views
Normalize ChIP-seq samples with different signal-to-noise ratio
csaw
edger
tmm
chipseq
updated 3.4 years ago by
Rory Stark
★ 5.2k • written 3.4 years ago by
maria.soler
• 0
1
vote
1
reply
1.5k
views
DiffBind scoreCol value question
DiffBind
ChIPSeq
chipseq
updated 3.7 years ago by
Rory Stark
★ 5.2k • written 3.7 years ago by
erbrocato
• 0
0
votes
0
replies
1.1k
views
findOverlapsOfPeaks - peaklist of connectedPeaks="min:
findOverlapsOfPeaks
ChIPpeakAnno
chipseq
3.7 years ago
Nadav
• 0
0
votes
0
replies
1.3k
views
DiffBind spike-in normalisation with varying amounts of spike-in chromatin
DiffBind
ChIPSeq
Normalization
SpikeIn
3.9 years ago
Drew
• 0
0
votes
6
replies
2.8k
views
cel files with affy library
ChIPSeq
updated 4.0 years ago by
almaza24map
• 0 • written 4.0 years ago by
scipio04
• 0
3
votes
12
replies
4.9k
views
Is it possible to change how DiffBind merge peaks?
DiffBind
ChIPseq
updated 4.0 years ago by
Rory Stark
★ 5.2k • written 5.9 years ago by
zhenfeng.liu1
▴ 20
0
votes
2
replies
1.7k
views
Using both spike in and TMM normalizations in ChIP-seq samples
ChIPSeq
SpikeIn
edgeR
Normalization
4.1 years ago • updated 4.0 years ago
maria.soler
• 0
2
votes
3
replies
2.2k
views
An error using Diffbind plotprofile
ChIPSeq
profileplyr
DiffBind
updated 4.0 years ago by
doug.barrows
▴ 20 • written 4.1 years ago by
zhuyi05
• 0
5
votes
8
replies
3.1k
views
how to construct a DBA object from count matrix
ChIPSeq
ATACSeq
differentially_occupied
DiffBind
updated 3.2 years ago by
Johanna Hardin
▴ 20 • written 4.1 years ago by
pegah.taklifi
▴ 30
0
votes
1
reply
2.5k
views
DiffBind Normalisation between Narrow/Broad Peaks from different peak callers
ChIPSeq
SICER2
DiffBind
MACS2
offtopic
updated 4.2 years ago by
James W. MacDonald
68k • written 4.2 years ago by
Yuan Tian
▴ 290
2
votes
5
replies
5.4k
views
News:
New in DiffBind 3.2: dba.plotProfile() - Peak profiles and profile heatmaps
profileplyr
ATACSeq
DiffBind
ComplexHeatmap
ChIPSeq
updated 2.7 years ago by
Junsik
• 0 • written 4.2 years ago by
Rory Stark
★ 5.2k
2
votes
4
replies
1.8k
views
could not duplicate the fragment length in "Reads to Regions" csaw tutorial
chipseq
csaw;
crosscorrelation
4.3 years ago • updated 4.2 years ago
richardallenfriedmanbrooklyn
▴ 30
194 results • Page
1 of 4
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Comment: Updated Support Site Editor
by
vs
• 0
Thanks for posting this comment, I had the same issue and was able to solve it with the ASCII clue. I am a non-native speaker of English, a…
Comment: Using DESeq2 on single cell RNA Seq data of same cell type but different conditi
by
ATpoint
★ 4.9k
No, cells from the same donor are correlated due to the donor effect. There is literature on this you should read to get started. https:/…
Comment: Using DESeq2 on single cell RNA Seq data of same cell type but different conditi
by
Raya
• 0
Wouldn't each sample in the single cell rna seq act as a biological replicate? each condition (eg: mab3_20C) has ~70 single cell samples.
Comment: Getting way too many DEGs with LRT for time-series RNA-seq!
by
James W. MacDonald
68k
>Sequential post-exposure measurements of the same set of genes is not the same thing as having multiple treated groups! They are not the…
Comment: Getting way too many DEGs with LRT for time-series RNA-seq!
by
Denise
• 0
Sequential post-exposure measurements of the same set of genes is not the same thing as having multiple treated groups! And I suppose ther…
Votes
Comment: Updated Support Site Editor
Updated Support Site Editor
Comment: Updated Support Site Editor
Comment: DESeq2 used with zinbwave weights - Differences on contrasts calculations
Comment: DESeq2 used with zinbwave weights - Differences on contrasts calculations
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