Showing : chipseq • reset
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Job: Postdoctoral Research Position in Cancer Genomics at Dana-Farber Cancer Institute/Harvard University
cancer computational biology rnaseq chipseq Job
written 11.2 years ago by • 0
0
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2
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606
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Problem in Chip-seq data analysis using MACS3
chipseq MACSdata
updated 7 months ago by ★ 5.0k • written 7 months ago by • 0
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0
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1.1k
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Diffbind Analysis gives error during profile plotting stage. Error in value[[3L]](cond) : profileplyr error: Error: BiocParallel errors 1 remote…
chipseq profileplyr DiffBind
8 months ago Muhammad • 0
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0
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406
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I want my overlapping peaks to stop merging by default doing read counting (using DiffBind in R-studio)
peakoverlap mergingpeaks ChIPseq DiffBind
9 months ago atlanta • 0
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0
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399
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News: Introduction to Epigenomics data analysis with R and Bioconductor course (online) - 14th-18th April
chipseq MNaseSeq ATACSeq
9 months ago info ▴ 10
1
vote
8
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2.9k
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[ChIP-seq] DESeq2 on counts matrix from union set of called peaks
csaw ChIPseq DESeq2 DiffBind
10 months ago • updated 9 months ago Luca • 0
1
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3
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1.3k
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Csaw normalization strategies - general inquiry
ChIPSeq csaw
updated 12 months ago by • 0 • written 12 months ago by • 0
6
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5
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2.4k
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MEDIPS for chIP-Seq
ChIPSeq
written 3.5 years ago by ▴ 30
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388
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ChIP peaks comparison
ChIPSeqData genomes ChIPSeq
14 months ago user_bioinfo • 0
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552
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Trying to understand basic DiffBind usage
ChIPSeq DiffBind
16 months ago Alejandro • 0
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0
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857
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Blacklist regions on DBA object (diffbind)
DiffBind chipseq
19 months ago gamma.jian ▴ 10
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0
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870
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DiffBind: no peaks in DBA object
DiffBind macs2 chipseq
21 months ago yvonneh • 0
0
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1
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625
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what is the sampleFiles
chipseq
updated 21 months ago by 68k • written 21 months ago by • 0
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872
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Best method for annotating distal peaks
ChIPSeq annotation ChIPpeakAnno
23 months ago nilanjanamani88 • 0
1
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3
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1.2k
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Big differences between biological replicates makes DESeq2 result 0
chipseq DifferentialMethylation DESeq2
updated 24 months ago by 43k • written 24 months ago by • 0
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651
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Parameter bSubControl with no effect in DiffBind dba.count?
bSubControl ChIPSeq DiffBind
2.0 years ago frueher • 0
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0
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1.0k
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Calculation of ChIP-seq normalization factors with non-conventional spike-in assumptions
csaw ChIPseq DiffBind
2.2 years ago jared.andrews07 ▴ 30
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1
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1.3k
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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 2.3 years ago by 68k • written 2.3 years ago by • 0
0
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841
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Why there are two pfms in the result of oligoSummary function of ChIPpeakAnno package?
ChIPpeakAnno ChIPSeq MotifDiscovery
2.3 years ago franciscrick41 • 0
2
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14
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2.7k
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ChIPpeakAnno: S.lycopersicum annotation missing
ChIPpeakAnno ChIPSeq
updated 2.4 years ago by 68k • written 2.4 years ago by ▴ 10
0
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5
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7.5k
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diffbind
DiffBind chipseq
updated 2.5 years ago by ★ 5.2k • written 2.5 years ago by • 0
1
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4
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2.4k
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DiffBind - Retrieving the differentially bound sites - HOW to calculate fold-change
ChIPSeq DiffBind
updated 2.6 years ago by ★ 5.2k • written 2.7 years ago by • 0
0
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2
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1.4k
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annotate peaks using a custom genome
ChIPSeq annotate ChIPpeakAnno
updated 2.7 years ago by ▴ 70 • written 2.8 years ago by ▴ 140
5
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8
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2.0k
views
Help with error install csaw
ChIPSeq ATACSeq
written 2.8 years ago by ▴ 20
0
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2
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2.2k
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DiffBind with ChIPseq from histone analysis: EdgeR or Deseq2?
DESeq2 ChIPSeq DiffBind edgeR HistoneModification
2.8 years ago Giulia • 0
0
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0
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861
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DiffBind with ChIPseq from histone analysis: EdgeR or Deseq2?
DESeq2 ChIPSeq DiffBind edgeR HistoneModification
2.8 years ago Giulia • 0
1
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2
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1.9k
views
how i can get the name of genes in pathway?
chipseq ChIPseeker
2.9 years ago chavaleab • 0
1
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3
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1.5k
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Only getting 10 peaks from mac2 callpeak
ChIPSeq
2.9 years ago stacy.genovese • 0
1
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4
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2.7k
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How to search a .narrowPeak file for a list of specific genes using GenomicRanges package
ChIPSeq PeakDetection
3.1 years ago • updated 3.0 years ago stacy.genovese • 0
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2
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1.6k
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New to ChipSeq getting 0 peaks using dba()
ChipSeq ChIPSeqData chipseqDB
3.2 years ago stacy.genovese • 0
0
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1
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1.4k
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DiffBind question _ SampleSheet / Venn diagram issue
chipseq DiffBind
updated 3.3 years ago by ★ 5.2k • written 3.3 years ago by • 0
0
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7
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3.0k
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CHIPQC error regarding BiocParallel
CHIPQC Diffbind chipseq rory stark Thomas Carroll
updated 3.5 years ago by ▴ 40 • written 5.8 years ago by ▴ 10
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1
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1.5k
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Job: 'Omics data analyst for HPCBio, University of Illinois
Metagenomics GenomicVariation Genomics RNASeq ChIPSeq
3.5 years ago Jenny Drnevich ★ 2.0k
0
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0
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1.3k
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intron coordination and annotation
ChIPSeq
updated 3.5 years ago by ★ 5.0k • written 3.5 years ago by • 0
0
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0
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1.4k
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Job: Bioinformatics Research Scientist- Epigenetics Group
HiC Epigenetics HiCHIP ChIPSeq
3.6 years ago xubeisi • 0
0
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1
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1.2k
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AssignChromosomeRegion not working in Rstudio 4.2
ChIPpeakAnno ChIPSeq
updated 3.7 years ago by ★ 1.3k • written 3.7 years ago by • 0
0
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3
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1.8k
views
DiffBind on static peak set for all samples
ChIPSeq DiffBind
updated 3.7 years ago by ★ 5.2k • written 3.7 years ago by • 0
0
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0
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1.2k
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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
3.7 years ago Swadha • 0
0
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3
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1.7k
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Input peak set for DiffBind should be all peaks or FDR filtered?
ChIPSeq DiffBind
written 3.9 years ago by • 0
1
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2
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2.3k
views
Normalize ChIP-seq samples with different signal-to-noise ratio
csaw edger tmm chipseq
updated 3.9 years ago by ★ 5.2k • written 3.9 years ago by • 0
1
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1
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1.7k
views
DiffBind scoreCol value question
DiffBind ChIPSeq chipseq
updated 4.1 years ago by ★ 5.2k • written 4.1 years ago by • 0
0
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0
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1.2k
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findOverlapsOfPeaks - peaklist of connectedPeaks="min:
findOverlapsOfPeaks ChIPpeakAnno chipseq
4.1 years ago Nadav • 0
0
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0
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1.4k
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DiffBind spike-in normalisation with varying amounts of spike-in chromatin
DiffBind ChIPSeq Normalization SpikeIn
4.3 years ago Drew • 0
0
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6
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3.1k
views
cel files with affy library
ChIPSeq
updated 4.5 years ago by • 0 • written 4.5 years ago by • 0
3
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12
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5.3k
views
Is it possible to change how DiffBind merge peaks?
DiffBind ChIPseq
updated 4.5 years ago by ★ 5.2k • written 6.4 years ago by ▴ 20
0
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2
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2.0k
views
Using both spike in and TMM normalizations in ChIP-seq samples
ChIPSeq SpikeIn edgeR Normalization
4.5 years ago maria.soler • 0
2
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3
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2.4k
views
An error using Diffbind plotprofile
ChIPSeq profileplyr DiffBind
updated 4.4 years ago by ▴ 20 • written 4.5 years ago by • 0
5
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8
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3.4k
views
how to construct a DBA object from count matrix
ChIPSeq ATACSeq differentially_occupied DiffBind
updated 3.6 years ago by ▴ 20 • written 4.5 years ago by ▴ 30
0
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1
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2.8k
views
DiffBind Normalisation between Narrow/Broad Peaks from different peak callers
ChIPSeq SICER2 DiffBind MACS2 offtopic
updated 4.7 years ago by 68k • written 4.7 years ago by ▴ 290
2
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5
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5.8k
views
News: New in DiffBind 3.2: dba.plotProfile() - Peak profiles and profile heatmaps
profileplyr ATACSeq DiffBind ComplexHeatmap ChIPSeq
updated 3.1 years ago by • 0 • written 4.7 years ago by ★ 5.2k
194 results • Page 1 of 4
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Comment: Bile acid analysis with limpa by ATpoint ★ 5.0k
Wilcox/Mann-Whitney-U cannot work because it is bound to sample size even when all of group X are lower than all of group Y. At 4 vs 3 the …
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I could install ChemmineOB on my MacBook Pro M1 Max using this procedure **1. Install open-babel and eigen using homebrew and create a cus…
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The design matrix that I described above is completely general. I imagine that it would be possible to use the same approach to generate fu…
Comment: Making a Full Rank Model for Allele-Specific Expression with DESeq2 by chp265 • 0
Cool, glad to hear I wasn't missing some functionality in DESeq2. I don't know that much about the differences between DESeq2 vs edgeR; my …
Comment: Making a Full Rank Model for Allele-Specific Expression with DESeq2 by Michael Love 43k
Yes, so for one thing, note that Gordon has provided code for doing what you are asking in edgeR, which you can go ahead and use. You aske…
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Answer: When to use edgeR or limma
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