Showing : ChIP-seq • reset
1
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231
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Error in dba.count and dba.analyze
DiffBind chip-seq differentially-binding-site
updated 9 months ago by ★ 4.0k • written 9 months ago by • 0
0
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2
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192
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ChIP-seq MA plot possibly skewed - how to normalise?
DiffBind MA plot normalization ChIP-seq
updated 12 months ago by ★ 4.0k • written 12 months ago by • 0
2
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7
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371
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Deferentially binding site is the same for all the samples
chip-seq diffBind sequence_analysis
updated 12 months ago by ★ 4.0k • written 12 months ago by • 0
0
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1
reply
108
views
Which internal tool does DiffBind uses to count BAM reads to calculate sizeFactor?
DiffBind ChIP-seq
updated 13 months ago by ★ 4.0k • written 14 months ago by ▴ 10
0
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1
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167
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use diffbind with normilized bedgraph files from spike ins
diffbind chip-seq chip spike spike-ins
updated 13 months ago by ★ 4.0k • written 15 months ago by • 0
0
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0
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135
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ChIPQC cross-coverage plot
chipqc chip-seq
15 months ago tuteja.reetu • 0
0
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0
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149
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Job: Bolzano, Italy: Post Doc Researcher in bioinformatics of cancer epigenomics
RNA-seq ChIP-seq Job
18 months ago Johannes Rainer ★ 1.9k
2
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1
reply
194
views
Using Input Samples in ChIP-seq Differential Analysis (csaw/edgeR)
csaw chip-seq
updated 19 months ago by ★ 27k • written 19 months ago by ▴ 710
1
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4
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384
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transcriptR ChIP-seq RNA-seq bam Error in mergeNamedAtomicVectors
TranscriptR RNA-seq ChIP-seq
updated 21 months ago by 57k • written 21 months ago by • 0
1
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4
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206
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in diffbind dba.peakset what is the meaning of minOverlap?
diffbind chip-seq dba.peakset
updated 21 months ago by ★ 4.0k • written 22 months ago by • 0
1
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1
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264
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Diffbind with age as blocking factor
diffbind chip-seq
updated 21 months ago by ★ 4.0k • written 22 months ago by ▴ 10
0
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0
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858
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Job: Senior/Junior Bioinformatician - University of Massachusetts Medical School
single cell sequencing RNA-Seq ChIP-Seq ATAC-Seq Job
2.1 years ago • updated 23 months ago Julie Zhu ★ 4.3k
2
votes
2
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602
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ChIPQC gives Bam file has 297 contigs Error: subscript contains out-of-bounds indices
ChIP-seq ChIPQC QC
updated 23 months ago by ▴ 20 • written 2.5 years ago by ▴ 10
0
votes
1
reply
704
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Reading peaks from MACS2 with DiffBind
chip-seq peak calling diffbind
updated 2.2 years ago by ★ 4.0k • written 2.2 years ago by • 0
0
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0
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367
views
Recommendation for visualizing ChIP-qPCR data?
R chip-seq histone chip-seq ggbio
2.6 years ago Ramiro Magno ▴ 100
2
votes
2
replies
465
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Using microarray re-annotation to combine array and Chip-Seq data
re-annotation affymetrix microarrays chip-seq affymetrix mouse gene arrays
2.7 years ago 2323982403 ▴ 50
0
votes
3
replies
320
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normalization of ChIP-seq data
normalization chip-seq
2.7 years ago Bogdan ▴ 620
0
votes
4
replies
508
views
csaw spike-in normalization
ChIP-seq csaw
updated 2.8 years ago by ★ 27k • written 2.8 years ago by ▴ 260
0
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0
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317
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How to properly use and understand chip-seq analysis with DiffBind ?
diffbind chip-seq R
2.8 years ago pierre.marin • 0
0
votes
2
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418
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csaw normalization and library size
chip-seq normalization
updated 3.0 years ago by ★ 27k • written 3.0 years ago by ▴ 260
0
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7
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771
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Compute average score across multiple bed files
chip-seq granges R bed files
updated 3.0 years ago by • 0 • written 3.0 years ago by • 0
3
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6
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692
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ChIP peak annotation: how to get all genes that overlap each peak?
ChIP-seq chippeakanno chipseeker
3.0 years ago 94133 • 0
0
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5
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618
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CSAW Spike In Normalization: Error in .local(object, ...) : library sizes of 'se.out' and 'object' are not identical
csaw software error R chip-seq bioconductor
updated 3.2 years ago by ★ 27k • written 3.2 years ago by • 0
1
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1
reply
1.2k
views
Importing Chip-Seq Peak MACS2 output (.xls) files into DBA object with Diffbind?
diffbind macs2 chip-seq
3.7 years ago chunhong.liu07 ▴ 10
0
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0
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620
views
ChIPQC: Error in names(res) <- nms
ChIPQC chip-seq
3.7 years ago nbkingsley • 0
1
vote
5
replies
1.0k
views
Problem reading Bed file using dba.count in DiffBind
DiffBind dba.count Chip-Seq Differential analysis
updated 4 months ago by • 0 • written 3.9 years ago by ▴ 40
0
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2
replies
593
views
Differential ChIP-seq with csaw: How to normalise counts on repetitive regions (telomers)?
csaw histone chip-seq chip-seq
updated 3.9 years ago by ★ 27k • written 3.9 years ago by • 0
1
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2
replies
682
views
Errors with makeTxDbFromBiomart
chip-seq
updated 3.9 years ago by 15k • written 3.9 years ago by • 0
0
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1
reply
836
views
Soggi regionPlot function gave error when import bigwig file with "percentOfRegion" mode
soGGi chip-seq region
updated 3.9 years ago by ▴ 400 • written 4.0 years ago by • 0
2
votes
11
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1.3k
views
Exporting normalized counts over final DB windows from csaw
csaw edger chip-seq
updated 4.0 years ago by 7.6k • written 4.0 years ago by • 0
2
votes
2
replies
642
views
How to use Diffbind as complete beginner?
diffbind chip-seq
updated 4.1 years ago by ▴ 630 • written 4.1 years ago by ▴ 10
0
votes
1
reply
846
views
Chip-seq peak annotation [Chipseeker]
chipseeker chip-seq annotation Guangchuang
updated 4.1 years ago by ★ 1.2k • written 4.1 years ago by • 0
0
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0
replies
504
views
Meta-Analysis chip-seq data
chip-seq meta-analysis
4.1 years ago rezapanahi222 • 0
3
votes
2
replies
487
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statistical tests to show the specificity of a phenomenon (eg increase in H3K27me3 mark)
chip-seq
updated 4.4 years ago by 13k • written 4.4 years ago by ▴ 620
0
votes
2
replies
922
views
Visualizing Normalization in DiffBind using MA: Differences between DESEQ2 / EdgeR & full v. effective library size
diffbind edger deseq2 chip-seq
updated 4.5 years ago by ★ 4.0k • written 4.5 years ago by • 0
0
votes
3
replies
1.1k
views
Clarification on Normalization Approach in DiffBind's db.analyze()
diffbind chip-seq normalization deseq2 tmm
updated 4.5 years ago by ★ 4.0k • written 4.5 years ago by • 0
3
votes
4
replies
997
views
Interpretation of cross correlation plot to determine fragment length
csaw chip-seq histone
updated 4.6 years ago by ★ 27k • written 4.6 years ago by • 0
3
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2
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1.3k
views
Removing GC content bias and trended bias from ChIP-seq data
csaw chip-seq normalization edger cqn
updated 4.8 years ago by ★ 27k • written 4.8 years ago by ▴ 10
0
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1
reply
611
views
DiffBind: Different results with different chromosome names
diffbind chip-seq
updated 4.9 years ago by ★ 4.0k • written 4.9 years ago by • 0
0
votes
3
replies
731
views
Chip-seq analysis with input
chip-seq differential binding analysis
updated 5.0 years ago by ★ 27k • written 5.0 years ago by • 0
0
votes
3
replies
2.5k
views
DiffBind Analysis with more than 2 samples?
diffbind chip-seq
updated 5.0 years ago by ★ 4.0k • written 5.0 years ago by • 0
0
votes
2
replies
878
views
Subtracting INPUT reads from ChIP read counts.
diffbind ChIP-seq
updated 5.1 years ago by ★ 4.0k • written 5.1 years ago by • 0
0
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6
replies
1.1k
views
Normalization - DESeq2 for Differential Binding using ChIP-seq data
deseq2 chip-seq Differential binding
5.1 years ago p2016k • 0
1
vote
18
replies
1.9k
views
Normalization of chip-seq data in manually specified regions using CSAW
chip-seq TSS TMM csaw
updated 5.2 years ago by ★ 27k • written 5.2 years ago by ▴ 10
0
votes
0
replies
637
views
Job: Post-doctoral position in algorithms for cancer data analysis
algorithms ChIP-seq cancer Job
5.2 years ago valentina.boeva • 0
2
votes
1
reply
618
views
How does csaw handle multiply aligned reads?
csaw chip-seq
updated 5.2 years ago by ★ 27k • written 5.2 years ago by ▴ 30
0
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0
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752
views
Job: Bioinformatics position at the Department of Genetics, Stanford, California
next-generation sequencing rna-seq chip-seq single cell Job
5.2 years ago Katja Hebestreit ▴ 130
0
votes
2
replies
1.3k
views
Diffbind plotting on contrasts
diffbind chip-seq
updated 5.5 years ago by ▴ 100 • written 6.5 years ago by • 0
0
votes
1
reply
1.4k
views
diffBind - bam not accessible
diffbind chip-seq bam
5.8 years ago eli7javasky • 0
3
votes
9
replies
1.7k
views
ChIPQC and broadPeak input
chipseq chipqc chip-seq
5.9 years ago lindahove ▴ 10
50 results • Page 1 of 1
Recent ...
Replies
Comment: featureCounts - paired-end data by Yanfang • 0
Hey Wei shi, May I ask you something related to featureCounts? I have only paired end reads (RNAseq) mapping to its genome by bowtie2, an…
Comment: WGCNA adjust p value by Kevin Blighe 3.2k
Cross-posted: https://www.biostars.org/p/9482927/
Comment: Unique GPos taking into account mcols by Marcel Ramos 540
Hi @maltethodberg We currently do not have a method that does this. Perhaps a `duplicated` method is appropriate but I am not the develop…
Comment: What are these genes ? [How to get Ensembl IDs for them] by abf ▴ 30
Mouse genes are not typically all capitals, but I was able to find a reference to a mouse gene in NCBI to [CH36-217G15][1]. Maybe this is …
Comment: Apparent Ensembl - Entrez gene mis-match in org.Mm.eg.db. by abf ▴ 30
I should note that when I query org.Mm.eg.db using the gene Symbols associated with my differential expression data I find a 1:1 correspond…
Votes
Comment: Idea: Using DESeq2 to test a change in ratio of two genes
A: Normalized counts of DESeq2 affected by design formula?
A: Finding orthologous human/mouse ENSEMBL IDs
Comment: What are these genes ? [How to get Ensembl IDs for them]
Answer: What lfcSE is dependent upon?
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