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 11.1 years ago by • 0
0
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2
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561
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Problem in Chip-seq data analysis using MACS3
chipseq MACSdata
updated 5 months ago by ★ 5.0k • written 5 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
6 months ago Muhammad • 0
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354
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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
8 months ago atlanta • 0
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346
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News: Introduction to Epigenomics data analysis with R and Bioconductor course (online) - 14th-18th April
chipseq MNaseSeq ATACSeq
8 months ago info ▴ 10
1
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8
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2.7k
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[ChIP-seq] DESeq2 on counts matrix from union set of called peaks
csaw ChIPseq DESeq2 DiffBind
9 months ago • updated 8 months ago Luca • 0
1
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3
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1.2k
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Csaw normalization strategies - general inquiry
ChIPSeq csaw
updated 10 months ago by • 0 • written 10 months ago by • 0
6
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5
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2.3k
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MEDIPS for chIP-Seq
ChIPSeq
written 3.3 years ago by ▴ 30
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338
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ChIP peaks comparison
ChIPSeqData genomes ChIPSeq
13 months ago user_bioinfo • 0
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511
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Trying to understand basic DiffBind usage
ChIPSeq DiffBind
14 months ago Alejandro • 0
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812
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Blacklist regions on DBA object (diffbind)
DiffBind chipseq
17 months ago gamma.jian ▴ 10
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818
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DiffBind: no peaks in DBA object
DiffBind macs2 chipseq
19 months ago yvonneh • 0
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1
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599
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what is the sampleFiles
chipseq
updated 20 months ago by 68k • written 20 months ago by • 0
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816
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Best method for annotating distal peaks
ChIPSeq annotation ChIPpeakAnno
22 months ago nilanjanamani88 • 0
1
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3
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1.1k
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Big differences between biological replicates makes DESeq2 result 0
chipseq DifferentialMethylation DESeq2
updated 22 months ago by 43k • written 22 months ago by • 0
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604
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Parameter bSubControl with no effect in DiffBind dba.count?
bSubControl ChIPSeq DiffBind
22 months ago frueher • 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
2.1 years ago jared.andrews07 ▴ 30
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1.2k
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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 2.2 years ago by 68k • written 2.2 years ago by • 0
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Why there are two pfms in the result of oligoSummary function of ChIPpeakAnno package?
ChIPpeakAnno ChIPSeq MotifDiscovery
2.2 years ago franciscrick41 • 0
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14
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2.5k
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ChIPpeakAnno: S.lycopersicum annotation missing
ChIPpeakAnno ChIPSeq
updated 2.3 years ago by 68k • written 2.3 years ago by ▴ 10
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5
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7.4k
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diffbind
DiffBind chipseq
updated 2.4 years ago by ★ 5.2k • written 2.4 years ago by • 0
1
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4
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2.3k
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DiffBind - Retrieving the differentially bound sites - HOW to calculate fold-change
ChIPSeq DiffBind
updated 2.5 years ago by ★ 5.2k • written 2.5 years ago by • 0
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2
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1.3k
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annotate peaks using a custom genome
ChIPSeq annotate ChIPpeakAnno
updated 2.6 years ago by ▴ 70 • written 2.6 years ago by ▴ 140
5
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8
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1.9k
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Help with error install csaw
ChIPSeq ATACSeq
written 2.7 years ago by ▴ 20
0
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2
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2.1k
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DiffBind with ChIPseq from histone analysis: EdgeR or Deseq2?
DESeq2 ChIPSeq DiffBind edgeR HistoneModification
2.7 years ago Giulia • 0
0
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0
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837
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DiffBind with ChIPseq from histone analysis: EdgeR or Deseq2?
DESeq2 ChIPSeq DiffBind edgeR HistoneModification
2.7 years ago Giulia • 0
1
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2
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1.9k
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how i can get the name of genes in pathway?
chipseq ChIPseeker
2.8 years ago chavaleab • 0
1
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3
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1.4k
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Only getting 10 peaks from mac2 callpeak
ChIPSeq
2.8 years ago stacy.genovese • 0
1
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4
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2.4k
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How to search a .narrowPeak file for a list of specific genes using GenomicRanges package
ChIPSeq PeakDetection
2.9 years ago stacy.genovese • 0
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2
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1.5k
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New to ChipSeq getting 0 peaks using dba()
ChipSeq ChIPSeqData chipseqDB
3.0 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 3.2 years ago by ★ 5.2k • written 3.2 years ago by • 0
0
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7
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2.9k
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CHIPQC error regarding BiocParallel
CHIPQC Diffbind chipseq rory stark Thomas Carroll
updated 3.3 years ago by ▴ 40 • written 5.6 years ago by ▴ 10
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1.5k
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Job: 'Omics data analyst for HPCBio, University of Illinois
Metagenomics GenomicVariation Genomics RNASeq ChIPSeq
3.4 years ago • updated 3.3 years ago Jenny Drnevich ★ 2.0k
0
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1.3k
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intron coordination and annotation
ChIPSeq
updated 3.4 years ago by ★ 5.0k • written 3.4 years ago by • 0
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0
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1.3k
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Job: Bioinformatics Research Scientist- Epigenetics Group
HiC Epigenetics HiCHIP ChIPSeq
3.5 years ago xubeisi • 0
0
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1
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1.1k
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AssignChromosomeRegion not working in Rstudio 4.2
ChIPpeakAnno ChIPSeq
updated 3.6 years ago by ★ 1.3k • written 3.6 years ago by • 0
0
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3
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1.7k
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DiffBind on static peak set for all samples
ChIPSeq DiffBind
updated 3.6 years ago by ★ 5.2k • written 3.6 years ago by • 0
0
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0
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1.1k
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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
3.6 years ago Swadha • 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 3.7 years ago by • 0
1
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2
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2.2k
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Normalize ChIP-seq samples with different signal-to-noise ratio
csaw edger tmm chipseq
updated 3.7 years ago by ★ 5.2k • written 3.7 years ago by • 0
1
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1
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1.6k
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DiffBind scoreCol value question
DiffBind ChIPSeq chipseq
updated 4.0 years ago by ★ 5.2k • written 4.0 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
4.0 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
4.2 years ago Drew • 0
0
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6
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3.0k
views
cel files with affy library
ChIPSeq
updated 4.3 years ago by • 0 • written 4.3 years ago by • 0
3
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12
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5.1k
views
Is it possible to change how DiffBind merge peaks?
DiffBind ChIPseq
updated 4.3 years ago by ★ 5.2k • written 6.2 years ago by ▴ 20
0
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2
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1.9k
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Using both spike in and TMM normalizations in ChIP-seq samples
ChIPSeq SpikeIn edgeR Normalization
4.4 years ago • updated 4.3 years ago maria.soler • 0
2
votes
3
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2.4k
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An error using Diffbind plotprofile
ChIPSeq profileplyr DiffBind
updated 4.3 years ago by ▴ 20 • written 4.4 years ago by • 0
5
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8
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3.3k
views
how to construct a DBA object from count matrix
ChIPSeq ATACSeq differentially_occupied DiffBind
updated 3.5 years ago by ▴ 20 • written 4.4 years ago by ▴ 30
0
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1
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2.7k
views
DiffBind Normalisation between Narrow/Broad Peaks from different peak callers
ChIPSeq SICER2 DiffBind MACS2 offtopic
updated 4.5 years ago by 68k • written 4.5 years ago by ▴ 290
2
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5
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5.7k
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News: New in DiffBind 3.2: dba.plotProfile() - Peak profiles and profile heatmaps
profileplyr ATACSeq DiffBind ComplexHeatmap ChIPSeq
updated 3.0 years ago by • 0 • written 4.5 years ago by ★ 5.2k
194 results • Page 1 of 4
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Comment: DECIPHER DesignProbes unable to design FISH-probes by Erik Wright ▴ 150
Are the sequences aligned (i.e., the same width) before running `TileSeqs()`?
Comment: BiocParallel (and DESeq2) - wrong args for environment subassignment by Michael Love 43k
BTW, I tested with no issue on MacOS ARM on our previous github issue.
Answer: DESeq(dds, parallel=TRUE) wrong args for environment subassignment by Michael Love 43k
The DESeq2 error makes sense, as we've talked about, given that the simple `bplapply` isn't working in your setup. Maybe give the traceb…
Answer: PTM analysis in LIMPA by Gordon Smyth 53k
For PTM analysis, the usual quantification command dpcQuant() is replaced by dpcImpute(). Otherwise the limpa pipeline is the same as for a…
Answer: problem reading bam files into nucleR by James W. MacDonald 68k
The first step is to update to the current versions of R/Bioconductor and try again. It's possible that you have run into a bug that's alre…
Votes
C: DESeq2 Following RSEM
Upcoming Ensembl API and data access changes - new blog post available
Comment: Highly similar RNA-seq samples in PCA - pooling or technical duplication?
Answer: Large logFC but somewhat high FDR
Comment: upstream git branches of bioc-release
Awards • All
Popular Question to Gordon Smyth 53k
Commentator to sina.nassiri ▴ 130
Popular Question to Hervé Pagès 16k
Popular Question to jared.andrews07 ▴ 30
Popular Question to James W. MacDonald 68k
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