Showing : ChIpseq • reset
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95
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ChIP peaks comparison
ChIPSeqData genomes ChIPSeq
9 days ago user_bioinfo • 0
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191
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Trying to understand basic DiffBind usage
ChIPSeq DiffBind
8 weeks ago Alejandro • 0
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331
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Blacklist regions on DBA object (diffbind)
DiffBind chipseq
4 months ago gamma.jian ▴ 10
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0
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331
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DiffBind: no peaks in DBA object
DiffBind macs2 chipseq
6 months ago yvonneh • 0
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1
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291
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what is the sampleFiles
chipseq
updated 7 months ago by 67k • written 7 months ago by • 0
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456
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Best method for annotating distal peaks
ChIPSeq annotation ChIPpeakAnno
9 months ago nilanjanamani88 • 0
1
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3
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661
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Big differences between biological replicates makes DESeq2 result 0
chipseq DifferentialMethylation DESeq2
updated 9 months ago by 42k • written 9 months ago by • 0
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0
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349
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Parameter bSubControl with no effect in DiffBind dba.count?
bSubControl ChIPSeq DiffBind
10 months ago frueher • 0
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0
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608
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Calculation of ChIP-seq normalization factors with non-conventional spike-in assumptions
csaw ChIPseq DiffBind
12 months ago jared.andrews07 ▴ 30
1
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1
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741
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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 13 months ago by 67k • written 13 months ago by • 0
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0
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467
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Why there are two pfms in the result of oligoSummary function of ChIPpeakAnno package?
ChIPpeakAnno ChIPSeq MotifDiscovery
13 months ago franciscrick41 • 0
2
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14
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1.7k
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ChIPpeakAnno: S.lycopersicum annotation missing
ChIPpeakAnno ChIPSeq
updated 14 months ago by 67k • written 15 months ago by ▴ 10
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5
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6.3k
views
diffbind
DiffBind chipseq
updated 15 months ago by ★ 5.2k • written 15 months ago by • 0
1
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4
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1.6k
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DiffBind - Retrieving the differentially bound sites - HOW to calculate fold-change
ChIPSeq DiffBind
updated 17 months ago by ★ 5.2k • written 18 months ago by • 0
0
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2
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864
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annotate peaks using a custom genome
ChIPSeq annotate ChIPpeakAnno
updated 18 months ago by ▴ 70 • written 19 months ago by ▴ 140
5
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8
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1.4k
views
Help with error install csaw
ChIPSeq ATACSeq
written 19 months ago by ▴ 20
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2
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1.5k
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DiffBind with ChIPseq from histone analysis: EdgeR or Deseq2?
DESeq2 ChIPSeq DiffBind edgeR HistoneModification
20 months ago Giulia • 0
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0
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594
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DiffBind with ChIPseq from histone analysis: EdgeR or Deseq2?
DESeq2 ChIPSeq DiffBind edgeR HistoneModification
20 months ago Giulia • 0
1
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2
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1.4k
views
how i can get the name of genes in pathway?
chipseq ChIPseeker
20 months ago chavaleab • 0
1
vote
3
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936
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Only getting 10 peaks from mac2 callpeak
ChIPSeq
21 months ago stacy.genovese • 0
1
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4
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1.6k
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How to search a .narrowPeak file for a list of specific genes using GenomicRanges package
ChIPSeq PeakDetection
22 months ago stacy.genovese • 0
0
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2
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1.0k
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New to ChipSeq getting 0 peaks using dba()
ChipSeq ChIPSeqData chipseqDB
24 months ago • updated 23 months 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 2.1 years ago by ★ 5.2k • written 2.1 years ago by • 0
6
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3
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1.7k
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MEDIPS for chIP-Seq
ChIPSeq
written 2.3 years ago by ▴ 30
0
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7
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2.2k
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CHIPQC error regarding BiocParallel
CHIPQC Diffbind chipseq rory stark Thomas Carroll
updated 2.3 years ago by ▴ 40 • written 4.6 years ago by ▴ 10
0
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1
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1.1k
views
Job: 'Omics data analyst for HPCBio, University of Illinois
Metagenomics GenomicVariation Genomics RNASeq ChIPSeq
2.3 years ago Jenny Drnevich ★ 2.0k
0
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0
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922
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intron coordination and annotation
ChIPSeq
updated 2.3 years ago by ★ 4.5k • written 2.3 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
2.4 years ago xubeisi • 0
0
votes
1
reply
857
views
AssignChromosomeRegion not working in Rstudio 4.2
ChIPpeakAnno ChIPSeq
updated 2.5 years ago by ★ 1.3k • written 2.5 years ago by • 0
0
votes
3
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1.3k
views
DiffBind on static peak set for all samples
ChIPSeq DiffBind
updated 2.5 years ago by ★ 5.2k • written 2.5 years ago by • 0
0
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0
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852
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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
2.6 years ago Swadha • 0
0
votes
1
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1.1k
views
Input peak set for DiffBind should be all peaks or FDR filtered?
ChIPSeq DiffBind
updated 2.6 years ago by ★ 5.2k • written 2.7 years ago by • 0
1
vote
2
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1.6k
views
Normalize ChIP-seq samples with different signal-to-noise ratio
csaw edger tmm chipseq
updated 2.7 years ago by ★ 5.2k • written 2.7 years ago by • 0
1
vote
1
reply
1.3k
views
DiffBind scoreCol value question
DiffBind ChIPSeq chipseq
updated 2.9 years ago by ★ 5.2k • written 2.9 years ago by • 0
0
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0
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936
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findOverlapsOfPeaks - peaklist of connectedPeaks="min:
findOverlapsOfPeaks ChIPpeakAnno chipseq
2.9 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
3.1 years ago Drew • 0
0
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6
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2.2k
views
cel files with affy library
ChIPSeq
updated 3.3 years ago by • 0 • written 3.3 years ago by • 0
3
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12
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4.1k
views
Is it possible to change how DiffBind merge peaks?
DiffBind ChIPseq
updated 3.3 years ago by ★ 5.2k • written 5.2 years ago by ▴ 20
0
votes
2
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1.4k
views
Using both spike in and TMM normalizations in ChIP-seq samples
ChIPSeq SpikeIn edgeR Normalization
3.3 years ago maria.soler • 0
2
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3
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1.8k
views
An error using Diffbind plotprofile
ChIPSeq profileplyr DiffBind
updated 3.2 years ago by ▴ 20 • written 3.3 years ago by • 0
5
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8
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2.6k
views
how to construct a DBA object from count matrix
ChIPSeq ATACSeq differentially_occupied DiffBind
updated 2.4 years ago by ▴ 20 • written 3.3 years ago by ▴ 30
0
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1
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2.1k
views
DiffBind Normalisation between Narrow/Broad Peaks from different peak callers
ChIPSeq SICER2 DiffBind MACS2 offtopic
updated 3.5 years ago by 67k • written 3.5 years ago by ▴ 290
2
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5
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4.3k
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News: New in DiffBind 3.2: dba.plotProfile() - Peak profiles and profile heatmaps
profileplyr ATACSeq DiffBind ComplexHeatmap ChIPSeq
updated 23 months ago by • 0 • written 3.5 years ago by ★ 5.2k
2
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4
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1.5k
views
could not duplicate the fragment length in "Reads to Regions" csaw tutorial
chipseq csaw; crosscorrelation
3.5 years ago richardallenfriedmanbrooklyn ▴ 30
0
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0
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1.9k
views
Blacklist error at dba.analyze(dbObj)
DiffBind ChIPSeq
3.6 years ago Goku • 0
2
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6
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1.8k
views
Error with dba.count(dbObj) in DiffBind
DiffBind ChIPSeq
3.7 years ago • updated 3.6 years ago Goku • 0
0
votes
3
replies
1.2k
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 3.7 years ago by ▴ 780 • written 3.7 years ago by • 0
1
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4
replies
1.6k
views
DiffBind analysis on ChIP-Seq qata and design matrix
ChIPSeq DiffBind ExperimentalDesign
3.8 years ago • updated 3.7 years ago SFn • 0
0
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11
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2.3k
views
Problem in subtracting ChIP Seq experiment with the input using ChIPSeqSpike
chipseq ChIPSeqSpike
updated 3.8 years ago by • 0 • written 3.8 years ago by • 0
0
votes
2
replies
1.4k
views
DiffBind Error When using dba.count()
ChIP-Rx DiffBind chipseq
4.0 years ago • updated 3.9 years ago indi97 • 0
50 results • Page 1 of 1
Recent ...
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Comment: How to extract phastcons score for all protein coding genes and lncRNAs using Ge by Robert Castelo ★ 3.4k
Hi, this is a long comment thread on 4-year old post, please open a new post with you question. To increase the odds of getting useful answ…
Comment: DESeq2 rerun returns different results by ATpoint ★ 4.5k
DESeq2 is deterministic if you use same input, code and software versions. Make sure to version-control your environment by at least tracki…
Answer: [How to construct a model.matrix ] by Gordon Smyth 51k
> Initially, I simply used > `lm(Epigenetic_age ~ Age_group + Age + Sex + PC1 + PC2 + PC3 + PC4 + PC5 + B + CD4T + CD8T + Mono + NK + Neutr…
Comment: How to extract phastcons score for all protein coding genes and lncRNAs using Ge by rania.alanany • 0
Hi Robert, Thank you for the explanation, But I am still little bit confused, Is the annotation package (TxDb.Hsapiens.UCSC.hg38.knownGene)…
Comment: Merge Replicates vs Mixed Model by abadgerw • 0
@gabrielhoffman any insight?
Votes
A: Some questions for remove batch effect by using mnnCorrect
A: Recommendations for combining multiple 10x runs into one SingleCellExperiment
Answer: [How to construct a model.matrix ]
Answer: Handling biological replicates in DESeq2
Comment: biomaRt rnorvegicus_gene_ensembl not available anymore
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