Showing : ChIP-Seq • reset
3
votes
9
replies
2.9k
views
ChIPQC and broadPeak input
chipseq chipqc chip-seq
8.6 years ago lindahove ▴ 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 ★ 5.1k • written 3.8 years ago by ▴ 20
0
votes
7
replies
2.2k
views
Compute average score across multiple bed files
chip-seq granges R bed files
updated 5.7 years ago by • 0 • written 5.8 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
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
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 ★ 5.1k • written 7.3 years ago by • 0
0
votes
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
1
vote
4
replies
886
views
in diffbind dba.peakset what is the meaning of minOverlap?
diffbind chip-seq dba.peakset
updated 4.5 years ago by ★ 5.1k • written 4.6 years ago by ▴ 10
0
votes
1
reply
1.0k
views
DiffBind: Different results with different chromosome names
diffbind chip-seq
updated 7.6 years ago by ★ 5.1k • written 7.6 years ago by • 0
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
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
1.6k
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 ★ 5.1k • written 7.2 years ago by • 0
3
votes
2
replies
891
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
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
2
votes
2
replies
1.3k
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
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
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
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
1.9k
views
Diffbind plotting on contrasts
diffbind chip-seq
updated 8.2 years ago by ▴ 110 • written 9.3 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
2
votes
1
reply
996
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
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
0
votes
4
replies
1.9k
views
Subtracting INPUT reads from ChIP read counts.
diffbind ChIP-seq
updated 12 weeks ago by ★ 5.1k • written 7.8 years ago by • 0
0
votes
3
replies
4.0k
views
DiffBind Analysis with more than 2 samples?
diffbind chip-seq
updated 7.7 years ago by ★ 5.1k • written 7.7 years ago by • 0
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
2.7k
views
Reading peaks from MACS2 with DiffBind
chip-seq peak calling diffbind
updated 4.9 years ago by ★ 5.1k • written 4.9 years ago by • 0
1
vote
1
reply
823
views
Diffbind with age as blocking factor
diffbind chip-seq
updated 4.5 years ago by ★ 5.1k • written 4.5 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
2
votes
1
reply
933
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
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 ★ 5.1k • written 4.0 years ago by ▴ 10
0
votes
1
reply
502
views
Which internal tool does DiffBind uses to count BAM reads to calculate sizeFactor?
DiffBind ChIP-seq
updated 3.9 years ago by ★ 5.1k • written 3.9 years ago by ▴ 10
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 ★ 5.1k • written 3.8 years ago by • 0
1
vote
1
reply
922
views
Error in dba.count and dba.analyze
DiffBind chip-seq differentially-binding-site
updated 3.5 years ago by ★ 5.1k • written 3.5 years ago by ▴ 20
0
votes
1
reply
719
views
meta-gene profiles
ChIP-seq
updated 2.1 years ago by ▴ 60 • written 2.1 years ago by ▴ 670
1
vote
2
replies
924
views
Could it be possible to get an older version of ChIPQC?
ChIPQC ChIP-seq DiffBind Rory_Stark
21 months ago • updated 20 months ago etiennedanis • 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
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 ★ 5.1k • 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
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
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
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
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
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
5.4 years ago 2323982403 ▴ 60
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
0
votes
0
replies
844
views
Meta-Analysis chip-seq data
chip-seq meta-analysis
6.9 years ago rezapanahi222 • 0
0
votes
0
replies
981
views
Job: Post-doctoral position in algorithms for cancer data analysis
algorithms ChIP-seq cancer Job
7.9 years ago valentina.boeva • 0
0
votes
0
replies
872
views
Recommendation for visualizing ChIP-qPCR data?
R chip-seq histone chip-seq ggbio
5.4 years ago Ramiro Magno ▴ 100
0
votes
0
replies
1.2k
views
ChIPQC: Error in names(res) <- nms
ChIPQC chip-seq
6.4 years ago nbkingsley • 0
0
votes
0
replies
689
views
ChIPQC cross-coverage plot
chipqc chip-seq
4.0 years ago tuteja.reetu • 0
50 results • Page 1 of 1
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Comment: How to tell and visualize up/down regulation of pathways from clusterprofiler gs by Guangchuang Yu ★ 1.2k
an example is also presented in <https://pubmed.ncbi.nlm.nih.gov/34557778/>.
Comment: Trying to use enrichGO by Guido Hooiveld ★ 3.9k
Nothing would prevent you from using the `enrichGO` function (or any other function for over-representation analysis [ORA]) with only 14 ge…
Comment: Different Shrunk Log2FC according with reference by andrebolerbarros ▴ 20
Thanks @atpoint for your answer! The issue with that is then it severely hinders the possiblity of using `apeglm` shrinking approach, sinc…
Comment: featureCounts reports an error:"featureCounts: input-files.c:2890: SAM_pairer_ge by ATpoint ★ 4.0k
The error that is relevant is `Aborted (core dumped)`. This line 2890 refers to the C source code that throws the error, it is not relevant…
Answer: Different Shrunk Log2FC according with reference by ATpoint ★ 4.0k
Please see: https://support.bioconductor.org/p/p134551/ I asked basically the same before. In short, reference level might have an influ…
Votes
C: SGSeq: moving toward diffex from SGSeq analysis
DEXSeq-Error in FUN(X[[i]], ...) : subscript out of bounds
Subset DEXSeqDataSet In DEXSeq
How to get all possible comparisons in DiffBind
Comment: get BM error
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