Showing : ChIPSeq • reset
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News: Epigenomics data analysis with R and Bioconductor
chipseq MNaseSeq ATACSeq
7 hours ago info ▴ 10
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[ChIP-seq] DESeq2 on counts matrix from union set of called peaks
csaw ChIPseq DESeq2 DiffBind
22 days ago • updated 21 days ago Luca • 0
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3
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752
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Csaw normalization strategies - general inquiry
ChIPSeq csaw
updated 9 weeks ago by • 0 • written 9 weeks ago by • 0
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2.0k
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MEDIPS for chIP-Seq
ChIPSeq
written 2.7 years ago by ▴ 30
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208
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ChIP peaks comparison
ChIPSeqData genomes ChIPSeq
4 months ago user_bioinfo • 0
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302
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Trying to understand basic DiffBind usage
ChIPSeq DiffBind
6 months ago Alejandro • 0
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486
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Blacklist regions on DBA object (diffbind)
DiffBind chipseq
9 months ago gamma.jian ▴ 10
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493
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DiffBind: no peaks in DBA object
DiffBind macs2 chipseq
11 months ago yvonneh • 0
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382
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what is the sampleFiles
chipseq
updated 11 months ago by 68k • written 11 months ago by • 0
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599
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Best method for annotating distal peaks
ChIPSeq annotation ChIPpeakAnno
13 months ago nilanjanamani88 • 0
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3
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843
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Big differences between biological replicates makes DESeq2 result 0
chipseq DifferentialMethylation DESeq2
updated 14 months ago by 43k • written 14 months ago by • 0
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439
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Parameter bSubControl with no effect in DiffBind dba.count?
bSubControl ChIPSeq DiffBind
14 months ago frueher • 0
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746
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Calculation of ChIP-seq normalization factors with non-conventional spike-in assumptions
csaw ChIPseq DiffBind
16 months ago jared.andrews07 ▴ 30
1
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1
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934
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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 18 months ago by 68k • written 18 months ago by • 0
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565
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Why there are two pfms in the result of oligoSummary function of ChIPpeakAnno package?
ChIPpeakAnno ChIPSeq MotifDiscovery
18 months ago franciscrick41 • 0
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14
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2.0k
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ChIPpeakAnno: S.lycopersicum annotation missing
ChIPpeakAnno ChIPSeq
updated 19 months ago by 68k • written 19 months ago by ▴ 10
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diffbind
DiffBind chipseq
updated 20 months ago by ★ 5.2k • written 20 months ago by • 0
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4
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1.9k
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DiffBind - Retrieving the differentially bound sites - HOW to calculate fold-change
ChIPSeq DiffBind
updated 22 months ago by ★ 5.2k • written 22 months ago by • 0
0
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2
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1.0k
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annotate peaks using a custom genome
ChIPSeq annotate ChIPpeakAnno
updated 23 months ago by ▴ 70 • written 23 months ago by ▴ 140
5
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8
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1.6k
views
Help with error install csaw
ChIPSeq ATACSeq
written 2.0 years ago by ▴ 20
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2
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1.8k
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DiffBind with ChIPseq from histone analysis: EdgeR or Deseq2?
DESeq2 ChIPSeq DiffBind edgeR HistoneModification
2.0 years ago Giulia • 0
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670
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DiffBind with ChIPseq from histone analysis: EdgeR or Deseq2?
DESeq2 ChIPSeq DiffBind edgeR HistoneModification
2.0 years ago Giulia • 0
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2
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1.6k
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how i can get the name of genes in pathway?
chipseq ChIPseeker
2.1 years ago chavaleab • 0
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3
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1.1k
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Only getting 10 peaks from mac2 callpeak
ChIPSeq
2.1 years ago stacy.genovese • 0
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4
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1.9k
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How to search a .narrowPeak file for a list of specific genes using GenomicRanges package
ChIPSeq PeakDetection
2.2 years ago stacy.genovese • 0
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1.1k
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New to ChipSeq getting 0 peaks using dba()
ChipSeq ChIPSeqData chipseqDB
2.4 years ago stacy.genovese • 0
0
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1
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1.2k
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DiffBind question _ SampleSheet / Venn diagram issue
chipseq DiffBind
updated 2.5 years ago by ★ 5.2k • written 2.5 years ago by • 0
0
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7
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2.5k
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CHIPQC error regarding BiocParallel
CHIPQC Diffbind chipseq rory stark Thomas Carroll
updated 2.6 years ago by ▴ 40 • written 5.0 years ago by ▴ 10
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1.2k
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Job: 'Omics data analyst for HPCBio, University of Illinois
Metagenomics GenomicVariation Genomics RNASeq ChIPSeq
2.7 years ago Jenny Drnevich ★ 2.0k
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1.0k
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intron coordination and annotation
ChIPSeq
updated 2.7 years ago by ★ 4.8k • written 2.7 years ago by • 0
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1.1k
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Job: Bioinformatics Research Scientist- Epigenetics Group
HiC Epigenetics HiCHIP ChIPSeq
2.8 years ago xubeisi • 0
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1
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937
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AssignChromosomeRegion not working in Rstudio 4.2
ChIPpeakAnno ChIPSeq
updated 2.9 years ago by ★ 1.3k • written 2.9 years ago by • 0
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3
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DiffBind on static peak set for all samples
ChIPSeq DiffBind
updated 2.9 years ago by ★ 5.2k • written 2.9 years ago by • 0
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951
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Can we get an Average Profile of ChIP peaks binding to Transcription "START and STOP site" both in a single plot?
ChIPSeq ChIPseeker
2.9 years ago Swadha • 0
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1
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1.2k
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Input peak set for DiffBind should be all peaks or FDR filtered?
ChIPSeq DiffBind
updated 3.0 years ago by ★ 5.2k • written 3.1 years ago by • 0
1
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2
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1.8k
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Normalize ChIP-seq samples with different signal-to-noise ratio
csaw edger tmm chipseq
updated 3.0 years ago by ★ 5.2k • written 3.0 years ago by • 0
1
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1
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1.4k
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DiffBind scoreCol value question
DiffBind ChIPSeq chipseq
updated 3.3 years ago by ★ 5.2k • written 3.3 years ago by • 0
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1.0k
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findOverlapsOfPeaks - peaklist of connectedPeaks="min:
findOverlapsOfPeaks ChIPpeakAnno chipseq
3.3 years ago Nadav • 0
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0
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1.2k
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DiffBind spike-in normalisation with varying amounts of spike-in chromatin
DiffBind ChIPSeq Normalization SpikeIn
3.5 years ago Drew • 0
0
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6
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2.6k
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cel files with affy library
ChIPSeq
updated 3.6 years ago by • 0 • written 3.7 years ago by • 0
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12
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4.6k
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Is it possible to change how DiffBind merge peaks?
DiffBind ChIPseq
updated 3.6 years ago by ★ 5.2k • written 5.5 years ago by ▴ 20
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2
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1.6k
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Using both spike in and TMM normalizations in ChIP-seq samples
ChIPSeq SpikeIn edgeR Normalization
3.7 years ago • updated 3.6 years ago maria.soler • 0
2
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3
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2.0k
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An error using Diffbind plotprofile
ChIPSeq profileplyr DiffBind
updated 3.6 years ago by ▴ 20 • written 3.7 years ago by • 0
5
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8
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2.9k
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how to construct a DBA object from count matrix
ChIPSeq ATACSeq differentially_occupied DiffBind
updated 2.8 years ago by ▴ 20 • written 3.7 years ago by ▴ 30
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1
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2.3k
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DiffBind Normalisation between Narrow/Broad Peaks from different peak callers
ChIPSeq SICER2 DiffBind MACS2 offtopic
updated 3.9 years ago by 68k • written 3.9 years ago by ▴ 290
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5
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5.0k
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News: New in DiffBind 3.2: dba.plotProfile() - Peak profiles and profile heatmaps
profileplyr ATACSeq DiffBind ComplexHeatmap ChIPSeq
updated 2.3 years ago by • 0 • written 3.9 years ago by ★ 5.2k
2
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4
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1.7k
views
could not duplicate the fragment length in "Reads to Regions" csaw tutorial
chipseq csaw; crosscorrelation
3.9 years ago • updated 3.8 years ago richardallenfriedmanbrooklyn ▴ 30
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2.1k
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Blacklist error at dba.analyze(dbObj)
DiffBind ChIPSeq
4.0 years ago Goku • 0
2
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6
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1.9k
views
Error with dba.count(dbObj) in DiffBind
DiffBind ChIPSeq
4.0 years ago Goku • 0
0
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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 4.1 years ago by ▴ 780 • written 4.1 years ago by • 0
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Deploy powerful missiles that generate large-scale explosions, resulting in the [solar smash online][1] formation of substantial craters on…
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Interesting data! Looking at these genes, it's like navigating a complex maze. The fluctuating values remind me of chasing high scores in […
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Can you provide more details on when this is happening? The salmon index is the definitive hash associated with the quant files, so I'm con…
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Oh wait. You want to map from Ensembl to NCBI? That's hard to do with model organisms, let alone non-model. This `OrgDb` doesn't have Ensem…
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Comment: Gene IDs conversion between Ensembl and NCBI nomenclature for non-model species
what the test method for enrichGO in clusterProfiler?
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Comment: plyranges: find exact GRanges match keeping metadata columns
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