Showing : chipseq • reset
0
votes
1
reply
96
views
what is the sampleFiles
chipseq
updated 8 days ago by 65k • written 8 days ago by • 0
0
votes
0
replies
149
views
Best method for annotating distal peaks
ChIPSeq annotation ChIPpeakAnno
10 weeks ago nilanjanamani88 • 0
1
vote
3
replies
370
views
Big differences between biological replicates makes DESeq2 result 0
chipseq DifferentialMethylation DESeq2
updated 11 weeks ago by 41k • written 12 weeks ago by • 0
0
votes
0
replies
164
views
Parameter bSubControl with no effect in DiffBind dba.count?
bSubControl ChIPSeq DiffBind
3 months ago frueher • 0
0
votes
0
replies
319
views
Calculation of ChIP-seq normalization factors with non-conventional spike-in assumptions
csaw ChIPseq DiffBind
5 months ago jared.andrews07 ▴ 30
1
vote
1
reply
432
views
DiffBind - how to prep the sample matrix when multiple bam files are used by MACS2's -t and -c param?
DiffBind chipseq
updated 6 months ago by 65k • written 6 months ago by • 0
0
votes
0
replies
273
views
Why there are two pfms in the result of oligoSummary function of ChIPpeakAnno package?
ChIPpeakAnno ChIPSeq MotifDiscovery
7 months ago franciscrick41 • 0
2
votes
14
replies
1.1k
views
ChIPpeakAnno: S.lycopersicum annotation missing
ChIPpeakAnno ChIPSeq
updated 8 months ago by 65k • written 8 months ago by ▴ 10
0
votes
5
replies
2.9k
views
diffbind
DiffBind chipseq
updated 9 months ago by ★ 5.1k • written 9 months ago by • 0
1
vote
4
replies
996
views
DiffBind - Retrieving the differentially bound sites - HOW to calculate fold-change
ChIPSeq DiffBind
updated 10 months ago by ★ 5.1k • written 11 months ago by • 0
0
votes
2
replies
591
views
annotate peaks using a custom genome
ChIPSeq annotate ChIPpeakAnno
updated 12 months ago by ▴ 70 • written 12 months ago by ▴ 140
5
votes
8
replies
1.0k
views
Help with error install csaw
ChIPSeq ATACSeq
written 13 months ago by • 0
0
votes
0
replies
441
views
DiffBind with ChIPseq from histone analysis: EdgeR or Deseq2?
DESeq2 ChIPSeq DiffBind edgeR HistoneModification
13 months ago Giulia • 0
0
votes
2
replies
1.1k
views
DiffBind with ChIPseq from histone analysis: EdgeR or Deseq2?
DESeq2 ChIPSeq DiffBind edgeR HistoneModification
13 months ago Giulia • 0
1
vote
2
replies
1.0k
views
how i can get the name of genes in pathway?
chipseq ChIPseeker
13 months ago chavaleab • 0
1
vote
3
replies
677
views
Only getting 10 peaks from mac2 callpeak
ChIPSeq
14 months ago stacy.genovese • 0
1
vote
4
replies
1.1k
views
How to search a .narrowPeak file for a list of specific genes using GenomicRanges package
ChIPSeq PeakDetection
15 months ago stacy.genovese • 0
0
votes
2
replies
756
views
New to ChipSeq getting 0 peaks using dba()
ChipSeq ChIPSeqData chipseqDB
17 months ago stacy.genovese • 0
0
votes
1
reply
859
views
DiffBind question _ SampleSheet / Venn diagram issue
chipseq DiffBind
updated 18 months ago by ★ 5.1k • written 18 months ago by • 0
6
votes
3
replies
1.3k
views
MEDIPS for chIP-Seq
ChIPSeq
written 20 months ago by ▴ 30
0
votes
1
reply
897
views
Job: 'Omics data analyst for HPCBio, University of Illinois
Metagenomics GenomicVariation Genomics RNASeq ChIPSeq
21 months ago • updated 20 months ago Jenny Drnevich ★ 2.0k
0
votes
0
replies
685
views
intron coordination and annotation
ChIPSeq
updated 21 months ago by ★ 4.0k • written 21 months ago by • 0
0
votes
0
replies
783
views
Job: Bioinformatics Research Scientist- Epigenetics Group
HiC Epigenetics HiCHIP ChIPSeq
22 months ago xubeisi • 0
0
votes
1
reply
697
views
AssignChromosomeRegion not working in Rstudio 4.2
ChIPpeakAnno ChIPSeq
updated 23 months ago by ★ 1.3k • written 23 months ago by • 0
0
votes
3
replies
1.0k
views
DiffBind on static peak set for all samples
ChIPSeq DiffBind
updated 23 months ago by ★ 5.1k • written 23 months ago by • 0
0
votes
0
replies
683
views
Can we get an Average Profile of ChIP peaks binding to Transcription "START and STOP site" both in a single plot?
ChIPSeq ChIPseeker
24 months ago Swadha • 0
1
vote
2
replies
1.2k
views
Normalize ChIP-seq samples with different signal-to-noise ratio
csaw edger tmm chipseq
updated 2.1 years ago by ★ 5.1k • written 2.1 years ago by • 0
0
votes
1
reply
846
views
Input peak set for DiffBind should be all peaks or FDR filtered?
ChIPSeq DiffBind
updated 2.0 years ago by ★ 5.1k • written 2.1 years ago by • 0
1
vote
1
reply
1.0k
views
DiffBind scoreCol value question
DiffBind ChIPSeq chipseq
updated 2.3 years ago by ★ 5.1k • written 2.4 years ago by • 0
0
votes
0
replies
732
views
findOverlapsOfPeaks - peaklist of connectedPeaks="min:
findOverlapsOfPeaks ChIPpeakAnno chipseq
2.4 years ago Nadav • 0
0
votes
0
replies
897
views
DiffBind spike-in normalisation with varying amounts of spike-in chromatin
DiffBind ChIPSeq Normalization SpikeIn
2.6 years ago Drew • 0
0
votes
6
replies
1.7k
views
cel files with affy library
ChIPSeq
updated 2.7 years ago by • 0 • written 2.7 years ago by • 0
0
votes
2
replies
1.1k
views
Using both spike in and TMM normalizations in ChIP-seq samples
ChIPSeq SpikeIn edgeR Normalization
2.7 years ago maria.soler • 0
2
votes
3
replies
1.4k
views
An error using Diffbind plotprofile
ChIPSeq profileplyr DiffBind
updated 2.6 years ago by ▴ 20 • written 2.7 years ago by • 0
5
votes
8
replies
2.1k
views
how to construct a DBA object from count matrix
ChIPSeq ATACSeq differentially_occupied DiffBind
updated 22 months ago by ▴ 20 • written 2.8 years ago by ▴ 30
0
votes
1
reply
1.8k
views
DiffBind Normalisation between Narrow/Broad Peaks from different peak callers
ChIPSeq SICER2 DiffBind MACS2 offtopic
updated 2.9 years ago by 65k • written 2.9 years ago by ▴ 280
2
votes
5
replies
3.3k
views
News: New in DiffBind 3.2: dba.plotProfile() - Peak profiles and profile heatmaps
profileplyr ATACSeq DiffBind ComplexHeatmap ChIPSeq
updated 16 months ago by • 0 • written 2.9 years ago by ★ 5.1k
2
votes
4
replies
1.2k
views
could not duplicate the fragment length in "Reads to Regions" csaw tutorial
chipseq csaw; crosscorrelation
3.0 years ago • updated 2.9 years ago richardallenfriedmanbrooklyn ▴ 20
0
votes
0
replies
1.7k
views
Blacklist error at dba.analyze(dbObj)
DiffBind ChIPSeq
3.1 years ago Goku • 0
2
votes
6
replies
1.4k
views
Error with dba.count(dbObj) in DiffBind
DiffBind ChIPSeq
3.1 years ago Goku • 0
0
votes
3
replies
1.0k
views
Which library now contains the ssdCoverage command that used to be found in the htseqtools package for R version 4.0.1 ?
Deprecation chipseq htseqtools Bioconductor
updated 3.1 years ago by ▴ 780 • written 3.1 years ago by • 0
1
vote
4
replies
1.3k
views
DiffBind analysis on ChIP-Seq qata and design matrix
ChIPSeq DiffBind ExperimentalDesign
3.2 years ago • updated 3.1 years ago SFn • 0
0
votes
11
replies
2.0k
views
Problem in subtracting ChIP Seq experiment with the input using ChIPSeqSpike
chipseq ChIPSeqSpike
updated 3.2 years ago by • 0 • written 3.3 years ago by • 0
0
votes
2
replies
1.1k
views
DiffBind Error When using dba.count()
ChIP-Rx DiffBind chipseq
3.4 years ago indi97 • 0
2
votes
2
replies
2.4k
views
ChIP seeker annotation error
DiffBind chipseq ChIPseeker ChipDb annotation
3.4 years ago • updated 3.2 years ago Mar Mar ▴ 20
1
vote
1
reply
1.5k
views
News: Extensive updates in DiffBind 3.0
Normalization ATACSeq ChIPSeq DiffBind chipseq
written 3.5 years ago by ★ 5.1k
1
vote
9
replies
3.0k
views
Spike-in normalization in EdgeR
CUTandRUN edgeR Normalization SpikeIn ChIPSeq
updated 17 months ago by ▴ 670 • written 3.5 years ago by ▴ 10
0
votes
1
reply
1.4k
views
How to use peak summits instead of TSS or transcript to plot heatmap for other factors
ChIPseqR ChIPs ChIPseeker ChIPSeq chipseq
updated 3.5 years ago by 65k • written 3.5 years ago by • 0
0
votes
7
replies
1.8k
views
CHIPQC error regarding BiocParallel
CHIPQC Diffbind chipseq rory stark Thomas Carroll
updated 20 months ago by ▴ 40 • written 4.0 years ago by ▴ 10
1
vote
7
replies
2.3k
views
DiffBind: dealing with replicates
diffbind chipseq
updated 4.1 years ago by ★ 5.1k • written 4.1 years ago by • 0
50 results • Page 1 of 1
Recent ...
Replies
Comment: get BM error by Fara • 0
Thank you for your response. The primary reason for translating Ensembl IDs into Entrez Gene IDs is to perform KEGG (Kyoto Encyclopedia of…
Comment: Error for AnnotationForge makeOrgPackageFromNCBI function by James W. MacDonald 65k
That's weird. I don't have any problem at all generating the `OrgDb` on my box. How big is the gene2pubmed.gz file? I get this: ``` gzip -…
Answer: get BM error by James W. MacDonald 65k
The genes you present are orthologous mappings from D. rerio to other teleost fishes, so it is probably going to be difficult to map to NCB…
Answer: How to retrieve gene ontology GO class from gene list? by James W. MacDonald 65k
You can also use a combination of the `org.Hs.eg.db` and `GO.db` packages. ``` > library(GO.db) > library(org.Hs.eg.db) > go <- m…
Comment: Different Shrunk Log2FC according with reference by Michael Love 41k
I took a look and the posterior width for these (fairly rare) examples overlaps zero. So the posterior when it disagrees is not narrow. An…
Votes
Answer: get BM error
Answer: Use of negative binomial model for exponential decay rate estimation using DESeq
Comment: Different Shrunk Log2FC according with reference
Reproducibility issue with scran together with lapply and BiocParallel
C: SGSeq: moving toward diffex from SGSeq analysis
Awards • All
Popular Question to Bine ▴ 40
Scholar to ATpoint ★ 4.0k
Popular Question to Gordon Smyth 50k
Popular Question to i.sudbery ▴ 40
Scholar to Michael Love 41k
Locations • All
United States, 2 minutes ago
China/Guangzhou/Southern Medical University, 2 minutes ago
Sweden, 3 minutes ago
Germany, 5 minutes ago
Portugal, 8 minutes ago
Traffic: 1006 users visited in the last hour
Content Search
Users
Tags
Badges
Help About
FAQ
Access RSS
API
Stats

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.

Powered by the version 2.3.6