Showing : Chip-seq • reset
0
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3
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4.0k
views
DiffBind Analysis with more than 2 samples?
diffbind chip-seq
updated 7.7 years ago by ★ 5.2k • written 7.7 years ago by • 0
1
vote
18
replies
3.2k
views
Normalization of chip-seq data in manually specified regions using CSAW
chip-seq TSS TMM csaw
updated 7.9 years ago by ★ 28k • written 7.9 years ago by ▴ 10
3
votes
9
replies
2.9k
views
ChIPQC and broadPeak input
chipseq chipqc chip-seq
8.6 years ago lindahove ▴ 10
0
votes
1
reply
2.7k
views
Reading peaks from MACS2 with DiffBind
chip-seq peak calling diffbind
updated 4.9 years ago by ★ 5.2k • written 4.9 years ago by • 0
1
vote
5
replies
2.4k
views
Problem reading Bed file using dba.count in DiffBind
DiffBind dba.count Chip-Seq Differential analysis
updated 3.1 years ago by • 0 • written 6.6 years ago by ▴ 40
0
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1
reply
2.4k
views
diffBind - bam not accessible
diffbind chip-seq bam
8.5 years ago eli7javasky • 0
3
votes
11
replies
2.3k
views
Exporting normalized counts over final DB windows from csaw
csaw edger chip-seq
updated 6.7 years ago by ★ 7.9k • written 6.7 years ago by ▴ 10
4
votes
2
replies
2.2k
views
Removing GC content bias and trended bias from ChIP-seq data
csaw chip-seq normalization edger cqn
updated 7.5 years ago by ★ 28k • written 7.5 years ago by ▴ 20
1
vote
1
reply
2.2k
views
Importing Chip-Seq Peak MACS2 output (.xls) files into DBA object with Diffbind?
diffbind macs2 chip-seq
6.4 years ago chunhong.liu07 ▴ 10
0
votes
7
replies
2.2k
views
Compute average score across multiple bed files
chip-seq granges R bed files
updated 5.8 years ago by • 0 • written 5.8 years ago by • 0
0
votes
4
replies
1.9k
views
Subtracting INPUT reads from ChIP read counts.
diffbind ChIP-seq
updated 3 months ago by ★ 5.2k • written 7.8 years ago by • 0
0
votes
3
replies
1.9k
views
Clarification on Normalization Approach in DiffBind's db.analyze()
diffbind chip-seq normalization deseq2 tmm
updated 7.3 years ago by ★ 5.2k • written 7.3 years ago by • 0
3
votes
4
replies
1.9k
views
Interpretation of cross correlation plot to determine fragment length
csaw chip-seq histone
updated 7.3 years ago by ★ 28k • written 7.3 years ago by • 0
0
votes
2
replies
1.9k
views
Diffbind plotting on contrasts
diffbind chip-seq
updated 8.2 years ago by ▴ 110 • written 9.3 years ago by • 0
0
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6
replies
1.8k
views
Normalization - DESeq2 for Differential Binding using ChIP-seq data
deseq2 chip-seq Differential binding
7.9 years ago p2016k • 0
0
votes
6
replies
1.7k
views
performing the differential binding in ChIP-seq
ChIP-seq
updated 12 months ago by • 0 • written 23 months ago by ▴ 670
1
vote
2
replies
1.6k
views
Errors with makeTxDbFromBiomart
chip-seq
updated 6.6 years ago by 16k • written 6.6 years ago by • 0
3
votes
6
replies
1.6k
views
ChIP peak annotation: how to get all genes that overlap each peak?
ChIP-seq chippeakanno chipseeker
5.8 years ago 94133 • 0
3
votes
4
replies
1.6k
views
RiP RLE normalisation using spike-in peaks in DiffBind for ChIP-seq
DiffBind SpikeIn Normalization ChIP-seq csaw
16 months ago • updated 15 months ago spg • 0
0
votes
2
replies
1.6k
views
Visualizing Normalization in DiffBind using MA: Differences between DESEQ2 / EdgeR & full v. effective library size
diffbind edger deseq2 chip-seq
updated 7.2 years ago by ★ 5.2k • written 7.2 years ago by • 0
4
votes
4
replies
1.6k
views
Strand-aware CSAW analysis
csaw chip-seq clip-seq
9.2 years ago IV ▴ 30
0
votes
1
reply
1.5k
views
Soggi regionPlot function gave error when import bigwig file with "percentOfRegion" mode
soGGi chip-seq region
updated 6.7 years ago by ▴ 420 • written 6.8 years ago by • 0
0
votes
0
replies
1.5k
views
Job: Senior/Junior Bioinformatician - University of Massachusetts Medical School
single cell sequencing RNA-Seq ChIP-Seq ATAC-Seq Job
4.8 years ago • updated 4.7 years ago Julie Zhu ★ 4.3k
0
votes
1
reply
1.4k
views
Chip-seq peak annotation [Chipseeker]
chipseeker chip-seq annotation Guangchuang
updated 6.9 years ago by ★ 1.2k • written 6.9 years ago by • 0
0
votes
4
replies
1.4k
views
csaw spike-in normalization
ChIP-seq csaw
updated 5.5 years ago by ★ 28k • written 5.5 years ago by ▴ 260
0
votes
5
replies
1.4k
views
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 5.9 years ago by ★ 28k • written 5.9 years ago by • 0
2
votes
2
replies
1.4k
views
How to use Diffbind as complete beginner?
diffbind chip-seq
updated 6.8 years ago by ▴ 650 • written 6.8 years ago by ▴ 10
2
votes
2
replies
1.3k
views
ChIPQC gives Bam file has 297 contigs Error: subscript contains out-of-bounds indices
ChIP-seq ChIPQC QC
updated 4.7 years ago by ▴ 20 • written 5.2 years ago by ▴ 10
1
vote
4
replies
1.3k
views
transcriptR ChIP-seq RNA-seq bam Error in mergeNamedAtomicVectors
TranscriptR RNA-seq ChIP-seq
updated 4.5 years ago by 65k • written 4.5 years ago by • 0
0
votes
1
reply
1.3k
views
News: Course Announcement: Use R / Bioconductor for Sequence Analysis (Intermediate Course)
Course RNA-Seq Chip-seq Parallel News
9.2 years ago Martin Morgan 25k
0
votes
0
replies
1.3k
views
Job: Bioinformatics position at the Department of Genetics, Stanford, California
next-generation sequencing rna-seq chip-seq single cell Job
8.0 years ago Katja Hebestreit ▴ 130
0
votes
3
replies
1.3k
views
Chip-seq analysis with input
chip-seq differential binding analysis
updated 7.7 years ago by ★ 28k • written 7.7 years ago by • 0
0
votes
1
reply
1.3k
views
use diffbind with normilized bedgraph files from spike ins
diffbind chip-seq chip spike spike-ins
updated 3.9 years ago by ★ 5.2k • written 4.0 years ago by ▴ 10
2
votes
7
replies
1.3k
views
Deferentially binding site is the same for all the samples
chip-seq diffBind sequence_analysis
updated 3.8 years ago by ★ 5.2k • written 3.8 years ago by ▴ 20
0
votes
2
replies
1.2k
views
HOMER error: Where is the file?
HOMER chip-seq
updated 18 months ago by ★ 4.0k • written 18 months ago by • 0
2
votes
1
reply
1.2k
views
problem with characters in chromosome names in DiffBind dba
DiffBind ChIP-Seq
updated 9.4 years ago by ★ 5.2k • written 9.4 years ago by ▴ 120
0
votes
2
replies
1.2k
views
Differential ChIP-seq with csaw: How to normalise counts on repetitive regions (telomers)?
csaw histone chip-seq chip-seq
updated 6.6 years ago by ★ 28k • written 6.6 years ago by • 0
2
votes
2
replies
1.2k
views
Using microarray re-annotation to combine array and Chip-Seq data
re-annotation affymetrix microarrays chip-seq affymetrix mouse gene arrays
5.5 years ago 2323982403 ▴ 60
0
votes
0
replies
1.2k
views
ChIPQC: Error in names(res) <- nms
ChIPQC chip-seq
6.4 years ago nbkingsley • 0
0
votes
2
replies
1.1k
views
ChIP-seq MA plot possibly skewed - how to normalise?
DiffBind MA plot normalization ChIP-seq
updated 3.8 years ago by ★ 5.2k • written 3.8 years ago by • 0
0
votes
1
reply
1.0k
views
DiffBind: Different results with different chromosome names
diffbind chip-seq
updated 7.6 years ago by ★ 5.2k • written 7.6 years ago by • 0
0
votes
2
replies
1.0k
views
csaw normalization and library size
chip-seq normalization
updated 5.7 years ago by ★ 28k • written 5.7 years ago by ▴ 260
2
votes
1
reply
997
views
How does csaw handle multiply aligned reads?
csaw chip-seq
updated 8.0 years ago by ★ 28k • written 8.0 years ago by ▴ 40
0
votes
0
replies
983
views
Job: Post-doctoral position in algorithms for cancer data analysis
algorithms ChIP-seq cancer Job
7.9 years ago valentina.boeva • 0
2
votes
1
reply
938
views
Using Input Samples in ChIP-seq Differential Analysis (csaw/edgeR)
csaw chip-seq
updated 4.4 years ago by ★ 28k • written 4.4 years ago by ★ 4.0k
1
vote
2
replies
932
views
Could it be possible to get an older version of ChIPQC?
ChIPQC ChIP-seq DiffBind Rory_Stark
21 months ago etiennedanis • 0
1
vote
1
reply
927
views
Error in dba.count and dba.analyze
DiffBind chip-seq differentially-binding-site
updated 3.5 years ago by ★ 5.2k • written 3.6 years ago by ▴ 20
0
votes
0
replies
909
views
How to properly use and understand chip-seq analysis with DiffBind ?
diffbind chip-seq R
5.6 years ago pierre.marin • 0
3
votes
2
replies
895
views
statistical tests to show the specificity of a phenomenon (eg increase in H3K27me3 mark)
chip-seq
updated 7.2 years ago by ★ 13k • written 7.2 years ago by ▴ 670
1
vote
4
replies
891
views
in diffbind dba.peakset what is the meaning of minOverlap?
diffbind chip-seq dba.peakset
updated 4.5 years ago by ★ 5.2k • written 4.6 years ago by ▴ 10
50 results • Page 1 of 1
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Answer: Dominance Index for Shotgun Metagenomics Data by Leo Lahti ▴ 40
1. Note that Simpson's dominance index (\lambda) is a different index than inverse Simpson (1/\lambda) or reciprocal Simpson (1-\lambda). T…
Comment: Math expression in shapeCustom legend in EnhancedVolcano by pl23 • 0
Thank you very much - that worked perfectly! Word of warning to those who try this: it screws up the other legends because of the markdown …
Answer: PCA plot suggestions by Michael Love 41k
For help with interpretation and design of analysis, I recommend working with a local statistician. Due to time restrictions, I can only…
Comment: DESeq2 Error in `.rowNamesDF<-`(x, value = value): Invalid 'row.names' length by ussarizona ▴ 10
Hi Michael, Yes, I could figure it out what does the error mean. In my matrix I had the first colum GeneID while in my condition I only h…
Answer: Deseq2. decontXcounts not integers. Useful alternative? by Michael Love 41k
Another option would be to put the per sample estimated contamination in the design. This is for example how RUV etc help remove spurious D…
Votes
Answer: Dominance Index for Shotgun Metagenomics Data
Answer: Math expression in shapeCustom legend in EnhancedVolcano
Comment: DESeq2 Error in `.rowNamesDF<-`(x, value = value): Invalid 'row.names' length
Comment: Deseq2. decontXcounts not integers. Useful alternative?
Comment: Opposite sign of LFC in count plots of DEGs (DESeq2)
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