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 11.0 years ago by • 0
0
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2
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506
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Problem in Chip-seq data analysis using MACS3
chipseq MACSdata
updated 4 months ago by ★ 5.0k • written 4 months ago by • 0
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988
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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
5 months ago Muhammad • 0
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0
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327
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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
6 months ago atlanta • 0
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313
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News: Introduction to Epigenomics data analysis with R and Bioconductor course (online) - 14th-18th April
chipseq MNaseSeq ATACSeq
6 months ago info ▴ 10
1
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8
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2.6k
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[ChIP-seq] DESeq2 on counts matrix from union set of called peaks
csaw ChIPseq DESeq2 DiffBind
7 months ago • updated 6 months ago Luca • 0
1
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3
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1.0k
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Csaw normalization strategies - general inquiry
ChIPSeq csaw
updated 8 months ago by • 0 • written 9 months ago by • 0
6
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5
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2.2k
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MEDIPS for chIP-Seq
ChIPSeq
written 3.2 years ago by ▴ 30
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311
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ChIP peaks comparison
ChIPSeqData genomes ChIPSeq
11 months ago user_bioinfo • 0
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467
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Trying to understand basic DiffBind usage
ChIPSeq DiffBind
13 months ago Alejandro • 0
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687
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Blacklist regions on DBA object (diffbind)
DiffBind chipseq
16 months ago gamma.jian ▴ 10
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738
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DiffBind: no peaks in DBA object
DiffBind macs2 chipseq
18 months ago yvonneh • 0
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1
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561
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what is the sampleFiles
chipseq
updated 18 months ago by 68k • written 18 months ago by • 0
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780
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Best method for annotating distal peaks
ChIPSeq annotation ChIPpeakAnno
20 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 21 months ago by 43k • written 21 months ago by • 0
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571
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Parameter bSubControl with no effect in DiffBind dba.count?
bSubControl ChIPSeq DiffBind
21 months ago frueher • 0
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943
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Calculation of ChIP-seq normalization factors with non-conventional spike-in assumptions
csaw ChIPseq DiffBind
23 months 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 2.1 years ago by 68k • written 2.1 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
2.1 years ago franciscrick41 • 0
2
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14
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2.4k
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ChIPpeakAnno: S.lycopersicum annotation missing
ChIPpeakAnno ChIPSeq
updated 2.2 years ago by 68k • written 2.2 years ago by ▴ 10
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5
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7.4k
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diffbind
DiffBind chipseq
updated 2.2 years ago by ★ 5.2k • written 2.3 years ago by • 0
1
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4
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2.2k
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DiffBind - Retrieving the differentially bound sites - HOW to calculate fold-change
ChIPSeq DiffBind
updated 2.4 years ago by ★ 5.2k • written 2.4 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 2.5 years ago by ▴ 70 • written 2.5 years ago by ▴ 140
5
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8
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1.8k
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Help with error install csaw
ChIPSeq ATACSeq
written 2.6 years ago by ▴ 20
0
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2
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2.0k
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DiffBind with ChIPseq from histone analysis: EdgeR or Deseq2?
DESeq2 ChIPSeq DiffBind edgeR HistoneModification
2.6 years ago Giulia • 0
0
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0
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809
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DiffBind with ChIPseq from histone analysis: EdgeR or Deseq2?
DESeq2 ChIPSeq DiffBind edgeR HistoneModification
2.6 years ago Giulia • 0
1
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2
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1.8k
views
how i can get the name of genes in pathway?
chipseq ChIPseeker
2.6 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
2.7 years ago stacy.genovese • 0
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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
2.8 years ago stacy.genovese • 0
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2
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1.4k
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New to ChipSeq getting 0 peaks using dba()
ChipSeq ChIPSeqData chipseqDB
2.9 years ago stacy.genovese • 0
0
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1
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1.3k
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DiffBind question _ SampleSheet / Venn diagram issue
chipseq DiffBind
updated 3.0 years ago by ★ 5.2k • written 3.0 years ago by • 0
0
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7
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2.8k
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CHIPQC error regarding BiocParallel
CHIPQC Diffbind chipseq rory stark Thomas Carroll
updated 3.2 years ago by ▴ 40 • written 5.5 years ago by ▴ 10
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1
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1.4k
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Job: 'Omics data analyst for HPCBio, University of Illinois
Metagenomics GenomicVariation Genomics RNASeq ChIPSeq
3.3 years ago • updated 3.2 years ago Jenny Drnevich ★ 2.0k
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1.2k
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intron coordination and annotation
ChIPSeq
updated 3.3 years ago by ★ 5.0k • written 3.3 years ago by • 0
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1.3k
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Job: Bioinformatics Research Scientist- Epigenetics Group
HiC Epigenetics HiCHIP ChIPSeq
3.4 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 3.4 years ago by ★ 1.3k • written 3.4 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 3.5 years ago by ★ 5.2k • written 3.5 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
3.5 years ago Swadha • 0
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2
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1.6k
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Input peak set for DiffBind should be all peaks or FDR filtered?
ChIPSeq DiffBind
written 3.6 years ago by • 0
1
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2
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2.1k
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Normalize ChIP-seq samples with different signal-to-noise ratio
csaw edger tmm chipseq
updated 3.6 years ago by ★ 5.2k • written 3.6 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 3.8 years ago by ★ 5.2k • written 3.9 years ago by • 0
0
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0
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1.1k
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findOverlapsOfPeaks - peaklist of connectedPeaks="min:
findOverlapsOfPeaks ChIPpeakAnno chipseq
3.9 years ago Nadav • 0
0
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0
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1.3k
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DiffBind spike-in normalisation with varying amounts of spike-in chromatin
DiffBind ChIPSeq Normalization SpikeIn
4.1 years ago Drew • 0
0
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6
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2.9k
views
cel files with affy library
ChIPSeq
updated 4.2 years ago by • 0 • written 4.2 years ago by • 0
3
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12
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5.0k
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Is it possible to change how DiffBind merge peaks?
DiffBind ChIPseq
updated 4.2 years ago by ★ 5.2k • written 6.1 years ago by ▴ 20
0
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2
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1.8k
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Using both spike in and TMM normalizations in ChIP-seq samples
ChIPSeq SpikeIn edgeR Normalization
4.2 years ago maria.soler • 0
2
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3
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2.3k
views
An error using Diffbind plotprofile
ChIPSeq profileplyr DiffBind
updated 4.1 years ago by ▴ 20 • written 4.2 years ago by • 0
5
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8
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3.2k
views
how to construct a DBA object from count matrix
ChIPSeq ATACSeq differentially_occupied DiffBind
updated 3.4 years ago by ▴ 20 • written 4.3 years ago by ▴ 30
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1
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2.6k
views
DiffBind Normalisation between Narrow/Broad Peaks from different peak callers
ChIPSeq SICER2 DiffBind MACS2 offtopic
updated 4.4 years ago by 68k • written 4.4 years ago by ▴ 290
2
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5
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5.5k
views
News: New in DiffBind 3.2: dba.plotProfile() - Peak profiles and profile heatmaps
profileplyr ATACSeq DiffBind ComplexHeatmap ChIPSeq
updated 2.9 years ago by • 0 • written 4.4 years ago by ★ 5.2k
194 results • Page 1 of 4
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Comment: Best practice for handling large data (matrix with >2^31-1 non-zero elements) in by James W. MacDonald 68k
Aaron already answered your question. If you have an HDF5 file, it will be read in as a `TENxMatrix` object, which isn't actually read in -…
Comment: Best practice for handling large data (matrix with >2^31-1 non-zero elements) in by dan.gatti • 0
Very strange. We have the same package versions. I tried adding the mtx.class, type, and delayed arguments, but it's still making the coun…
Comment: DESeq2 for candidate gene analysis by piffelpaff ▴ 20
thank you so much for answering Dr. Love!
Answer: DESeq2 for candidate gene analysis by Michael Love 43k
Your plan 1 is reasonable. Run DESeq2 on the whole dataset to obtain size factors and moderated dispersion estimates and then extract the u…
Comment: Best practice for handling large data (matrix with >2^31-1 non-zero elements) in by James W. MacDonald 68k
Oh. ``` > z <- read10xCounts(c(tmpdir, tmpdir), mtx.class = "SVT_SparseMatrix", delayed = TRUE) > class(counts(z)) [1] "DelayedMatrix" att…
Votes
A: Multi-level experiments in Limma
Answer: Should voomWithQualityWeights still be used when the sample-specific weights var
Answer: DESeq2 for candidate gene analysis
DESeq2 for candidate gene analysis
Answer: DESeq2 for candidate gene analysis
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