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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581
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Problem in Chip-seq data analysis using MACS3
chipseq MACSdata
updated 6 months ago by ★ 5.0k • written 6 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
7 months ago Muhammad • 0
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0
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372
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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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362
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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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2.8k
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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 11 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 3.4 years ago by ▴ 30
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351
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ChIP peaks comparison
ChIPSeqData genomes ChIPSeq
13 months ago user_bioinfo • 0
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522
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Trying to understand basic DiffBind usage
ChIPSeq DiffBind
15 months ago Alejandro • 0
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829
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Blacklist regions on DBA object (diffbind)
DiffBind chipseq
18 months ago gamma.jian ▴ 10
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838
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DiffBind: no peaks in DBA object
DiffBind macs2 chipseq
19 months ago yvonneh • 0
0
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1
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606
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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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827
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Best method for annotating distal peaks
ChIPSeq annotation ChIPpeakAnno
22 months ago nilanjanamani88 • 0
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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 23 months ago by 43k • written 23 months ago by • 0
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617
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Parameter bSubControl with no effect in DiffBind dba.count?
bSubControl ChIPSeq DiffBind
23 months 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
2.1 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
0
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0
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824
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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
2
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14
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2.6k
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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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7.5k
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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 2.6 years ago by ★ 5.2k • written 2.6 years ago by • 0
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 2.7 years ago by ▴ 70 • written 2.7 years ago by ▴ 140
5
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8
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1.9k
views
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
2.8 years ago Giulia • 0
0
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0
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845
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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
2.8 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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2.5k
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How to search a .narrowPeak file for a list of specific genes using GenomicRanges package
ChIPSeq PeakDetection
3.0 years ago • updated 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
3.1 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
views
CHIPQC error regarding BiocParallel
CHIPQC Diffbind chipseq rory stark Thomas Carroll
updated 3.4 years ago by ▴ 40 • written 5.7 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
3.4 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 3.4 years ago by ★ 5.0k • written 3.4 years ago by • 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
3.5 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
3.7 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 3.8 years ago by • 0
1
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2
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2.2k
views
Normalize ChIP-seq samples with different signal-to-noise ratio
csaw edger tmm chipseq
updated 3.8 years ago by ★ 5.2k • written 3.8 years ago by • 0
1
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1
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1.6k
views
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 4.4 years ago by • 0 • written 4.4 years ago by • 0
3
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12
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5.2k
views
Is it possible to change how DiffBind merge peaks?
DiffBind ChIPseq
updated 4.4 years ago by ★ 5.2k • written 6.3 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 maria.soler • 0
2
votes
3
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2.4k
views
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 4.6 years ago by 68k • written 4.6 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 4.6 years ago by ★ 5.2k
194 results • Page 1 of 4
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Answer: Question about RE-agnostic mode for intact Hi-C and Micro-C normalization(HiCDCP by victor04052024 • 0
You write quite well, and the content is very interesting. I'll provide you a link to my page [granny 2](https://granny2.io).
Answer: DESeq2 - how many surrogate variables from svaseq, use of lfcshrink by victor04052024 • 0
The information is interesting, and your writing is excellent. I will provide you a link to my website [Baseball bros](https://baseball-gam…
Comment: segfault in edgeR glmQLFit by Gordon Smyth 53k
We have committed a bug fix now to edgeR on both the release and developmental Bioconductor repositories.
Answer: Ensembl site unresponsive via biomaRt by horaortiz8 • 0
I appreciate the link. I'll get in touch with them directly; I wish they had a status page of some kind. https://www.ensembl.org/Help/Cont…
Comment: segfault in edgeR glmQLFit by Mark • 0
Thanks! We had been considering some of these adjustments as well, given the small number of features and total reads. Your advice is well-…
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
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