Showing : Chip-Seq • reset
3
votes
4
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1.8k
views
RiP RLE normalisation using spike-in peaks in DiffBind for ChIP-seq
DiffBind SpikeIn Normalization ChIP-seq csaw
18 months ago • updated 17 months ago spg • 0
0
votes
2
replies
1.3k
views
HOMER error: Where is the file?
HOMER chip-seq
updated 19 months ago by ★ 4.2k • written 19 months ago by • 0
1
vote
2
replies
1.0k
views
Could it be possible to get an older version of ChIPQC?
ChIPQC ChIP-seq DiffBind Rory_Stark
22 months ago etiennedanis • 0
0
votes
6
replies
1.8k
views
performing the differential binding in ChIP-seq
ChIP-seq
updated 14 months ago by • 0 • written 2.1 years ago by ▴ 670
0
votes
1
reply
808
views
meta-gene profiles
ChIP-seq
updated 2.3 years ago by ▴ 60 • written 2.3 years ago by ▴ 670
1
vote
1
reply
964
views
Error in dba.count and dba.analyze
DiffBind chip-seq differentially-binding-site
updated 3.7 years ago by ★ 5.2k • written 3.7 years ago by ▴ 20
0
votes
2
replies
1.1k
views
ChIP-seq MA plot possibly skewed - how to normalise?
DiffBind MA plot normalization ChIP-seq
updated 3.9 years ago by ★ 5.2k • written 3.9 years ago by • 0
2
votes
7
replies
1.3k
views
Deferentially binding site is the same for all the samples
chip-seq diffBind sequence_analysis
updated 3.9 years ago by ★ 5.2k • written 3.9 years ago by ▴ 20
0
votes
1
reply
528
views
Which internal tool does DiffBind uses to count BAM reads to calculate sizeFactor?
DiffBind ChIP-seq
updated 4.0 years ago by ★ 5.2k • written 4.1 years ago by ▴ 10
0
votes
1
reply
1.4k
views
use diffbind with normilized bedgraph files from spike ins
diffbind chip-seq chip spike spike-ins
updated 4.0 years ago by ★ 5.2k • written 4.1 years ago by ▴ 10
0
votes
0
replies
730
views
ChIPQC cross-coverage plot
chipqc chip-seq
4.2 years ago tuteja.reetu • 0
0
votes
0
replies
771
views
Job: Bolzano, Italy: Post Doc Researcher in bioinformatics of cancer epigenomics
RNA-seq ChIP-seq Job
4.4 years ago Johannes Rainer ★ 2.1k
2
votes
1
reply
977
views
Using Input Samples in ChIP-seq Differential Analysis (csaw/edgeR)
csaw chip-seq
updated 4.5 years ago by ★ 28k • written 4.5 years ago by ★ 4.2k
1
vote
4
replies
1.4k
views
transcriptR ChIP-seq RNA-seq bam Error in mergeNamedAtomicVectors
TranscriptR RNA-seq ChIP-seq
updated 4.6 years ago by 66k • written 4.6 years ago by ▴ 10
1
vote
4
replies
937
views
in diffbind dba.peakset what is the meaning of minOverlap?
diffbind chip-seq dba.peakset
updated 4.6 years ago by ★ 5.2k • written 4.7 years ago by ▴ 10
1
vote
1
reply
851
views
Diffbind with age as blocking factor
diffbind chip-seq
updated 4.6 years ago by ★ 5.2k • written 4.7 years ago by ▴ 10
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
5.0 years ago • updated 4.8 years ago Julie Zhu ★ 4.3k
2
votes
2
replies
1.4k
views
ChIPQC gives Bam file has 297 contigs Error: subscript contains out-of-bounds indices
ChIP-seq ChIPQC QC
updated 4.8 years ago by ▴ 20 • written 5.3 years ago by ▴ 10
0
votes
1
reply
2.8k
views
Reading peaks from MACS2 with DiffBind
chip-seq peak calling diffbind
updated 5.0 years ago by ★ 5.2k • written 5.0 years ago by • 0
0
votes
0
replies
903
views
Recommendation for visualizing ChIP-qPCR data?
R chip-seq histone chip-seq ggbio
5.5 years ago Ramiro Magno ▴ 100
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
5.6 years ago 2323982403 ▴ 60
0
votes
3
replies
888
views
normalization of ChIP-seq data
normalization chip-seq
5.6 years ago Bogdan ▴ 670
0
votes
4
replies
1.5k
views
csaw spike-in normalization
ChIP-seq csaw
updated 5.6 years ago by ★ 28k • written 5.6 years ago by ▴ 260
0
votes
0
replies
931
views
How to properly use and understand chip-seq analysis with DiffBind ?
diffbind chip-seq R
5.7 years ago pierre.marin • 0
0
votes
2
replies
1.1k
views
csaw normalization and library size
chip-seq normalization
updated 5.9 years ago by ★ 28k • written 5.9 years ago by ▴ 260
0
votes
7
replies
2.3k
views
Compute average score across multiple bed files
chip-seq granges R bed files
updated 5.9 years ago by • 0 • written 5.9 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
5.9 years ago 94133 • 0
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 6.1 years ago by ★ 28k • written 6.1 years ago by • 0
1
vote
1
reply
2.3k
views
Importing Chip-Seq Peak MACS2 output (.xls) files into DBA object with Diffbind?
diffbind macs2 chip-seq
6.5 years ago chunhong.liu07 ▴ 10
0
votes
0
replies
1.2k
views
ChIPQC: Error in names(res) <- nms
ChIPQC chip-seq
6.6 years ago nbkingsley • 0
1
vote
5
replies
2.5k
views
Problem reading Bed file using dba.count in DiffBind
DiffBind dba.count Chip-Seq Differential analysis
updated 3.2 years ago by • 0 • written 6.7 years ago by ▴ 40
0
votes
2
replies
1.3k
views
Differential ChIP-seq with csaw: How to normalise counts on repetitive regions (telomers)?
csaw histone chip-seq chip-seq
updated 6.7 years ago by ★ 28k • written 6.7 years ago by • 0
1
vote
2
replies
1.7k
views
Errors with makeTxDbFromBiomart
chip-seq
updated 6.7 years ago by 16k • written 6.7 years ago by • 0
0
votes
1
reply
1.5k
views
Soggi regionPlot function gave error when import bigwig file with "percentOfRegion" mode
soGGi chip-seq region
updated 6.8 years ago by ▴ 420 • written 6.9 years ago by • 0
3
votes
11
replies
2.4k
views
Exporting normalized counts over final DB windows from csaw
csaw edger chip-seq
updated 6.9 years ago by ★ 7.9k • written 6.9 years ago by ▴ 10
2
votes
2
replies
1.4k
views
How to use Diffbind as complete beginner?
diffbind chip-seq
updated 6.9 years ago by ▴ 670 • written 6.9 years ago by ▴ 10
0
votes
1
reply
1.5k
views
Chip-seq peak annotation [Chipseeker]
chipseeker chip-seq annotation Guangchuang
updated 7.0 years ago by ★ 1.2k • written 7.0 years ago by • 0
0
votes
0
replies
864
views
Meta-Analysis chip-seq data
chip-seq meta-analysis
7.0 years ago rezapanahi222 • 0
3
votes
2
replies
954
views
statistical tests to show the specificity of a phenomenon (eg increase in H3K27me3 mark)
chip-seq
updated 7.3 years ago by ★ 13k • written 7.3 years ago by ▴ 670
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 7.4 years ago by ★ 5.2k • written 7.4 years ago by • 0
0
votes
3
replies
2.0k
views
Clarification on Normalization Approach in DiffBind's db.analyze()
diffbind chip-seq normalization deseq2 tmm
updated 7.4 years ago by ★ 5.2k • written 7.4 years ago by • 0
3
votes
4
replies
2.0k
views
Interpretation of cross correlation plot to determine fragment length
csaw chip-seq histone
updated 7.4 years ago by ★ 28k • written 7.4 years ago by • 0
4
votes
2
replies
2.3k
views
Removing GC content bias and trended bias from ChIP-seq data
csaw chip-seq normalization edger cqn
updated 7.7 years ago by ★ 28k • written 7.7 years ago by ▴ 20
0
votes
1
reply
1.1k
views
DiffBind: Different results with different chromosome names
diffbind chip-seq
updated 7.8 years ago by ★ 5.2k • written 7.8 years ago by • 0
0
votes
3
replies
1.3k
views
Chip-seq analysis with input
chip-seq differential binding analysis
updated 7.9 years ago by ★ 28k • written 7.9 years ago by • 0
0
votes
3
replies
4.1k
views
DiffBind Analysis with more than 2 samples?
diffbind chip-seq
updated 7.9 years ago by ★ 5.2k • written 7.9 years ago by • 0
0
votes
4
replies
2.0k
views
Subtracting INPUT reads from ChIP read counts.
diffbind ChIP-seq
updated 4 months ago by ★ 5.2k • written 8.0 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
8.0 years ago p2016k • 0
1
vote
18
replies
3.3k
views
Normalization of chip-seq data in manually specified regions using CSAW
chip-seq TSS TMM csaw
updated 8.0 years ago by ★ 28k • written 8.0 years ago by ▴ 10
0
votes
0
replies
1.0k
views
Job: Post-doctoral position in algorithms for cancer data analysis
algorithms ChIP-seq cancer Job
8.0 years ago valentina.boeva • 0
50 results • Page 1 of 1
Recent ...
Replies
Comment: gds in GEOmetadb 2023-06-26 version is empty by Frederico Moraes Ferreira ▴ 100
Try axel -n 20 https://gbnci.cancer.gov/geo/GEOmetadb.sqlite.gz
Comment: Most enriched pathway is not expressed when modifying universe parameter by James W. MacDonald 66k
The default for `enrichGO` is to subset to those with a p-value<0.05. You don't adjust that default argument, so you shouldn't have any GO …
Answer: In a 3 group DEG analysis with three batches, can I use 1 group in all three bat by Michael Love 42k
You can compare A and C thanks to the sharing of samples from B across 1, 2 and 3.
Comment: Most enriched pathway is not expressed when modifying universe parameter by adripel • 0
In the enrichGO results we have significant and non-significant enriched terms that are displayed. So why would an enriched term (significa…
Answer: Design formula, numeric contrast, and lfcshrink in deseq2 by Michael Love 42k
For questions about how to construct the correct contrasts correspond to particular hypotheses, I recommend consulting with a local statist…
Votes
Time-course, comparison of two groups
Answer: Behaviour of featureCounts when quantifying multi-mapping reads
Answer: GESA with certain gene list returns no result with human genom, but many result
Answer: Odd behavior of Rsubread::featureCounts when setting `nonOverlap = 0`
Answer: DESeq2 returns results for group with just one replicate
Awards • All
Popular Question to Frederico Moraes Ferreira ▴ 100
Popular Question to richardallenfriedmanbrooklyn ▴ 20
Teacher to Michael Love 42k
Popular Question to Dario Strbenac ★ 1.5k
Scholar to James W. MacDonald 66k
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