Showing : chipseq • reset
1
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Csaw normalization strategies - general inquiry
ChIPSeq csaw
updated 2 days ago by • 0 • written 5 days ago by • 0
6
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5
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1.9k
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MEDIPS for chIP-Seq
ChIPSeq
written 2.5 years ago by ▴ 30
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0
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165
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ChIP peaks comparison
ChIPSeqData genomes ChIPSeq
12 weeks ago user_bioinfo • 0
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0
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253
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Trying to understand basic DiffBind usage
ChIPSeq DiffBind
4 months ago Alejandro • 0
0
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0
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417
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Blacklist regions on DBA object (diffbind)
DiffBind chipseq
7 months ago gamma.jian ▴ 10
0
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0
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416
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DiffBind: no peaks in DBA object
DiffBind macs2 chipseq
9 months ago yvonneh • 0
0
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1
reply
336
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what is the sampleFiles
chipseq
updated 9 months ago by 67k • written 9 months ago by • 0
0
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0
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530
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Best method for annotating distal peaks
ChIPSeq annotation ChIPpeakAnno
11 months ago nilanjanamani88 • 0
1
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3
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742
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Big differences between biological replicates makes DESeq2 result 0
chipseq DifferentialMethylation DESeq2
updated 12 months ago by 43k • written 12 months ago by • 0
0
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0
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401
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Parameter bSubControl with no effect in DiffBind dba.count?
bSubControl ChIPSeq DiffBind
12 months ago frueher • 0
0
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0
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679
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Calculation of ChIP-seq normalization factors with non-conventional spike-in assumptions
csaw ChIPseq DiffBind
14 months ago jared.andrews07 ▴ 30
1
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1
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826
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DiffBind - how to prep the sample matrix when multiple bam files are used by MACS2's -t and -c param?
DiffBind chipseq
updated 16 months ago by 67k • written 16 months ago by • 0
0
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0
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517
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Why there are two pfms in the result of oligoSummary function of ChIPpeakAnno package?
ChIPpeakAnno ChIPSeq MotifDiscovery
16 months ago franciscrick41 • 0
2
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14
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1.8k
views
ChIPpeakAnno: S.lycopersicum annotation missing
ChIPpeakAnno ChIPSeq
updated 17 months ago by 67k • written 17 months ago by ▴ 10
0
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5
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6.7k
views
diffbind
DiffBind chipseq
updated 18 months ago by ★ 5.2k • written 18 months ago by • 0
1
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4
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1.8k
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DiffBind - Retrieving the differentially bound sites - HOW to calculate fold-change
ChIPSeq DiffBind
updated 20 months ago by ★ 5.2k • written 20 months ago by • 0
0
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2
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946
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annotate peaks using a custom genome
ChIPSeq annotate ChIPpeakAnno
updated 21 months ago by ▴ 70 • written 21 months ago by ▴ 140
5
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8
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1.5k
views
Help with error install csaw
ChIPSeq ATACSeq
written 22 months ago by ▴ 20
0
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2
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1.7k
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DiffBind with ChIPseq from histone analysis: EdgeR or Deseq2?
DESeq2 ChIPSeq DiffBind edgeR HistoneModification
22 months ago Giulia • 0
0
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0
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636
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DiffBind with ChIPseq from histone analysis: EdgeR or Deseq2?
DESeq2 ChIPSeq DiffBind edgeR HistoneModification
22 months ago Giulia • 0
1
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2
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1.5k
views
how i can get the name of genes in pathway?
chipseq ChIPseeker
23 months ago chavaleab • 0
1
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3
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1.0k
views
Only getting 10 peaks from mac2 callpeak
ChIPSeq
23 months ago stacy.genovese • 0
1
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4
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1.7k
views
How to search a .narrowPeak file for a list of specific genes using GenomicRanges package
ChIPSeq PeakDetection
2.1 years ago • updated 2.0 years ago stacy.genovese • 0
0
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2
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1.1k
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New to ChipSeq getting 0 peaks using dba()
ChipSeq ChIPSeqData chipseqDB
2.2 years ago stacy.genovese • 0
0
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1
reply
1.1k
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DiffBind question _ SampleSheet / Venn diagram issue
chipseq DiffBind
updated 2.3 years ago by ★ 5.2k • written 2.3 years ago by • 0
0
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7
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2.4k
views
CHIPQC error regarding BiocParallel
CHIPQC Diffbind chipseq rory stark Thomas Carroll
updated 2.5 years ago by ▴ 40 • written 4.8 years ago by ▴ 10
0
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1
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1.2k
views
Job: 'Omics data analyst for HPCBio, University of Illinois
Metagenomics GenomicVariation Genomics RNASeq ChIPSeq
2.5 years ago Jenny Drnevich ★ 2.0k
0
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0
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969
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intron coordination and annotation
ChIPSeq
updated 2.5 years ago by ★ 4.6k • written 2.5 years ago by • 0
0
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0
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1.0k
views
Job: Bioinformatics Research Scientist- Epigenetics Group
HiC Epigenetics HiCHIP ChIPSeq
2.6 years ago xubeisi • 0
0
votes
1
reply
901
views
AssignChromosomeRegion not working in Rstudio 4.2
ChIPpeakAnno ChIPSeq
updated 2.7 years ago by ★ 1.3k • written 2.7 years ago by • 0
0
votes
3
replies
1.4k
views
DiffBind on static peak set for all samples
ChIPSeq DiffBind
updated 2.7 years ago by ★ 5.2k • written 2.7 years ago by • 0
0
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0
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900
views
Can we get an Average Profile of ChIP peaks binding to Transcription "START and STOP site" both in a single plot?
ChIPSeq ChIPseeker
2.8 years ago Swadha • 0
0
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1
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1.1k
views
Input peak set for DiffBind should be all peaks or FDR filtered?
ChIPSeq DiffBind
updated 2.8 years ago by ★ 5.2k • written 2.9 years ago by • 0
1
vote
2
replies
1.7k
views
Normalize ChIP-seq samples with different signal-to-noise ratio
csaw edger tmm chipseq
updated 2.9 years ago by ★ 5.2k • written 2.9 years ago by • 0
1
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1
reply
1.3k
views
DiffBind scoreCol value question
DiffBind ChIPSeq chipseq
updated 3.1 years ago by ★ 5.2k • written 3.1 years ago by • 0
0
votes
0
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980
views
findOverlapsOfPeaks - peaklist of connectedPeaks="min:
findOverlapsOfPeaks ChIPpeakAnno chipseq
3.2 years ago Nadav • 0
0
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0
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1.1k
views
DiffBind spike-in normalisation with varying amounts of spike-in chromatin
DiffBind ChIPSeq Normalization SpikeIn
3.3 years ago Drew • 0
0
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6
replies
2.4k
views
cel files with affy library
ChIPSeq
updated 3.5 years ago by • 0 • written 3.5 years ago by • 0
3
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12
replies
4.3k
views
Is it possible to change how DiffBind merge peaks?
DiffBind ChIPseq
updated 3.5 years ago by ★ 5.2k • written 5.4 years ago by ▴ 20
0
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2
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1.5k
views
Using both spike in and TMM normalizations in ChIP-seq samples
ChIPSeq SpikeIn edgeR Normalization
3.5 years ago maria.soler • 0
2
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3
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1.9k
views
An error using Diffbind plotprofile
ChIPSeq profileplyr DiffBind
updated 3.4 years ago by ▴ 20 • written 3.5 years ago by • 0
5
votes
8
replies
2.8k
views
how to construct a DBA object from count matrix
ChIPSeq ATACSeq differentially_occupied DiffBind
updated 2.6 years ago by ▴ 20 • written 3.5 years ago by ▴ 30
0
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1
reply
2.2k
views
DiffBind Normalisation between Narrow/Broad Peaks from different peak callers
ChIPSeq SICER2 DiffBind MACS2 offtopic
updated 3.7 years ago by 67k • written 3.7 years ago by ▴ 290
2
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5
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4.6k
views
News: New in DiffBind 3.2: dba.plotProfile() - Peak profiles and profile heatmaps
profileplyr ATACSeq DiffBind ComplexHeatmap ChIPSeq
updated 2.1 years ago by • 0 • written 3.7 years ago by ★ 5.2k
2
votes
4
replies
1.6k
views
could not duplicate the fragment length in "Reads to Regions" csaw tutorial
chipseq csaw; crosscorrelation
3.7 years ago richardallenfriedmanbrooklyn ▴ 30
0
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0
replies
2.0k
views
Blacklist error at dba.analyze(dbObj)
DiffBind ChIPSeq
3.9 years ago Goku • 0
2
votes
6
replies
1.8k
views
Error with dba.count(dbObj) in DiffBind
DiffBind ChIPSeq
3.9 years ago • updated 3.8 years ago Goku • 0
0
votes
3
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1.3k
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 3.9 years ago by ▴ 780 • written 3.9 years ago by • 0
1
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4
replies
1.7k
views
DiffBind analysis on ChIP-Seq qata and design matrix
ChIPSeq DiffBind ExperimentalDesign
4.0 years ago • updated 3.9 years ago SFn • 0
0
votes
11
replies
2.4k
views
Problem in subtracting ChIP Seq experiment with the input using ChIPSeqSpike
chipseq ChIPSeqSpike
updated 4.0 years ago by • 0 • written 4.0 years ago by • 0
50 results • Page 1 of 1
Recent ...
Replies
Comment: input for singR function by iamin053 • 0
Hi Paria, I'm wondering if you were able to get an answer on this please. I would greatly appreciate any comments!
Comment: build samplesheet and plot profile by yf • 0
![enter image description here][1] [1]: /media/images/8ea93bd0-bc90-443d-a332-4701f54a
Answer: I am having issues with bowtie2_build by James W. MacDonald 67k
Is proof.fa an actual FASTA file? Have you tried using the demo data that comes with the package? See the [vignette under Build Bowtie Inde…
Answer: DEG analysis across multiple timepoints, treatments and tissues by Michael Love 43k
Yes, if you think the entire time course can be modified by tissue effects then you would include another set of interaction terms. I re…
Comment: How to visualize these pathways using pathview by Guido Hooiveld ★ 4.1k
FYI: a similar, if not identical issue has been reported before (`pathview` has problems visualizing some pathways, but not all). You likel…
Votes
A: Doubt about the "zero expression" genes or genes with no reads at all in the co
Answer: Unable to install nloptr
Answer: ensembldb for Homo Sapiens organism containing superfluous SYMBOL genes?
C: How does edgeR cpm function calculate log(CPM) values?
Answer: Selection of correct coefficients or contrasts in DESeq2
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