Showing : ChIPseq • reset
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Chip Seq Analysis of RNA Polymerase 2
ChIPseeker ChIPSeqData ChIPSeq Bioconductor
written 4 weeks ago by • 0
0
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1
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3.3k
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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 11.3 years ago by • 0
0
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2
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650
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Problem in Chip-seq data analysis using MACS3
chipseq MACSdata
updated 8 months ago by ★ 5.0k • written 8 months ago by • 0
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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
9 months ago Muhammad • 0
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461
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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
11 months ago atlanta • 0
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0
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438
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News: Introduction to Epigenomics data analysis with R and Bioconductor course (online) - 14th-18th April
chipseq MNaseSeq ATACSeq
11 months ago info ▴ 10
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8
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3.0k
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[ChIP-seq] DESeq2 on counts matrix from union set of called peaks
csaw ChIPseq DESeq2 DiffBind
12 months ago • updated 11 months ago Luca • 0
1
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3
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1.4k
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Csaw normalization strategies - general inquiry
ChIPSeq csaw
updated 13 months ago by • 0 • written 13 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 3.6 years ago by ▴ 30
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419
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ChIP peaks comparison
ChIPSeqData genomes ChIPSeq
16 months ago user_bioinfo • 0
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590
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Trying to understand basic DiffBind usage
ChIPSeq DiffBind
17 months ago Alejandro • 0
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918
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Blacklist regions on DBA object (diffbind)
DiffBind chipseq
20 months ago gamma.jian ▴ 10
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917
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DiffBind: no peaks in DBA object
DiffBind macs2 chipseq
22 months ago yvonneh • 0
0
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1
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663
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what is the sampleFiles
chipseq
updated 23 months ago by 68k • written 23 months ago by • 0
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928
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Best method for annotating distal peaks
ChIPSeq annotation ChIPpeakAnno
2.1 years ago nilanjanamani88 • 0
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3
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1.3k
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Big differences between biological replicates makes DESeq2 result 0
chipseq DifferentialMethylation DESeq2
updated 2.1 years ago by 43k • written 2.1 years ago by • 0
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676
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Parameter bSubControl with no effect in DiffBind dba.count?
bSubControl ChIPSeq DiffBind
2.1 years ago frueher • 0
0
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0
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1.1k
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Calculation of ChIP-seq normalization factors with non-conventional spike-in assumptions
csaw ChIPseq DiffBind
2.3 years ago jared.andrews07 ▴ 30
1
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1
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1.4k
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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 2.4 years ago by 68k • written 2.4 years ago by • 0
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861
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Why there are two pfms in the result of oligoSummary function of ChIPpeakAnno package?
ChIPpeakAnno ChIPSeq MotifDiscovery
2.4 years ago franciscrick41 • 0
2
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14
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2.8k
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ChIPpeakAnno: S.lycopersicum annotation missing
ChIPpeakAnno ChIPSeq
updated 2.5 years ago by 68k • written 2.5 years ago by ▴ 10
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5
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7.5k
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diffbind
DiffBind chipseq
updated 2.6 years ago by ★ 5.3k • written 2.6 years ago by • 0
1
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4
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2.5k
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DiffBind - Retrieving the differentially bound sites - HOW to calculate fold-change
ChIPSeq DiffBind
updated 2.8 years ago by ★ 5.3k • written 2.8 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 2.9 years ago by ▴ 70 • written 2.9 years ago by ▴ 140
5
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8
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2.0k
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Help with error install csaw
ChIPSeq ATACSeq
written 3.0 years ago by ▴ 20
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2
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2.3k
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DiffBind with ChIPseq from histone analysis: EdgeR or Deseq2?
DESeq2 ChIPSeq DiffBind edgeR HistoneModification
3.0 years ago Giulia • 0
0
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0
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888
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DiffBind with ChIPseq from histone analysis: EdgeR or Deseq2?
DESeq2 ChIPSeq DiffBind edgeR HistoneModification
3.0 years ago Giulia • 0
1
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2
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2.0k
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how i can get the name of genes in pathway?
chipseq ChIPseeker
3.0 years ago chavaleab • 0
1
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3
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1.6k
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Only getting 10 peaks from mac2 callpeak
ChIPSeq
3.0 years ago stacy.genovese • 0
1
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4
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2.9k
views
How to search a .narrowPeak file for a list of specific genes using GenomicRanges package
ChIPSeq PeakDetection
3.2 years ago • updated 3.1 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
3.3 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 3.4 years ago by ★ 5.3k • written 3.4 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 3.6 years ago by ▴ 40 • written 5.9 years ago by ▴ 10
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1
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1.6k
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Job: 'Omics data analyst for HPCBio, University of Illinois
Metagenomics GenomicVariation Genomics RNASeq ChIPSeq
3.6 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 3.6 years ago by ★ 5.0k • written 3.6 years ago by • 0
0
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0
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1.5k
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Job: Bioinformatics Research Scientist- Epigenetics Group
HiC Epigenetics HiCHIP ChIPSeq
3.7 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 3.8 years ago by ★ 1.4k • written 3.8 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 3.8 years ago by ★ 5.3k • written 3.8 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
3.9 years ago Swadha • 0
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3
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1.8k
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Input peak set for DiffBind should be all peaks or FDR filtered?
ChIPSeq DiffBind
written 4.0 years ago by • 0
1
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2
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2.4k
views
Normalize ChIP-seq samples with different signal-to-noise ratio
csaw edger tmm chipseq
updated 4.0 years ago by ★ 5.3k • written 4.0 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 4.2 years ago by ★ 5.3k • written 4.2 years ago by • 0
0
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0
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1.3k
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findOverlapsOfPeaks - peaklist of connectedPeaks="min:
findOverlapsOfPeaks ChIPpeakAnno chipseq
4.3 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
4.4 years ago Drew • 0
0
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6
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3.4k
views
cel files with affy library
ChIPSeq
updated 4.6 years ago by • 0 • written 4.6 years ago by • 0
3
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12
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5.5k
views
Is it possible to change how DiffBind merge peaks?
DiffBind ChIPseq
updated 4.6 years ago by ★ 5.3k • written 6.5 years ago by ▴ 20
0
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2
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2.1k
views
Using both spike in and TMM normalizations in ChIP-seq samples
ChIPSeq SpikeIn edgeR Normalization
4.6 years ago maria.soler • 0
2
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3
replies
2.5k
views
An error using Diffbind plotprofile
ChIPSeq profileplyr DiffBind
updated 4.5 years ago by ▴ 20 • written 4.6 years ago by • 0
5
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8
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3.5k
views
how to construct a DBA object from count matrix
ChIPSeq ATACSeq differentially_occupied DiffBind
updated 3.7 years ago by ▴ 20 • written 4.6 years ago by ▴ 30
0
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1
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3.0k
views
DiffBind Normalisation between Narrow/Broad Peaks from different peak callers
ChIPSeq SICER2 DiffBind MACS2 offtopic
updated 4.8 years ago by 68k • written 4.8 years ago by ▴ 290
195 results • Page 1 of 4
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Comment: Inclusion of non-coding portions of transcripts (UTR-regions and introns) within by Pat • 0
Ill be honest, I didnt trust any of these services for a long time. Im a political science major and the pressure around writing is intense…
Comment: Question on processing compound protein groups in limpa by brianpeterson1210 • 0
Thank you[,][1] Appreciated! [1]: http://paint3d.org
Comment: Subsetting DDS object for individual conditions over time by A ▴ 60
Hi @atpoint Thank you for the quick reply! and this makes sense! I will confirm with a corr to see how the SFs differ but also how DE dif…
Answer: Subsetting DDS object for individual conditions over time by ATpoint ★ 5.0k
It would surprise my quite a bit if the size factors would differ notably between subset or not. I would always try to keep the size factor…
Comment: GSEA error by Adithi • 0
Thank you so much. That makes perfect sense to me. I will work on this.
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Comment: Question about using LRT test for time course experiments with DESeq2
A: DESeq2 LRT test for multi-factor designs
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