Showing : Csaw • reset
1
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3
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1.6k
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regionCounts() from csaw - object 'fancy_mseq' not found
ATACSeq regionCounts csaw
updated 5 months ago by • 0 • written 2.0 years ago by • 0
0
votes
0
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342
views
Calculation of ChIP-seq normalization factors with non-conventional spike-in assumptions
csaw ChIPseq DiffBind
6 months ago jared.andrews07 ▴ 30
0
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0
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353
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Csaw - WindowCount : Paired reads unexpectedly filtered out
windowCount csaw paired
10 months ago julie.chevalier • 0
2
votes
4
replies
936
views
Error with regionCounts()
csaw
13 months ago Chris ▴ 10
0
votes
0
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419
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some questions about eliminating efficiency biaes in csaw user's guide
csawUsersGuide csaw
15 months ago sashu • 0
3
votes
4
replies
1.7k
views
RiP RLE normalisation using spike-in peaks in DiffBind for ChIP-seq
DiffBind SpikeIn Normalization ChIP-seq csaw
17 months ago • updated 16 months ago spg • 0
0
votes
0
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457
views
normFactors or calcNormFactors (computing the normalization or scaling factors)
limma edgeR csaw
17 months ago Bogdan ▴ 670
1
vote
2
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1.2k
views
Normalize ChIP-seq samples with different signal-to-noise ratio
csaw edger tmm chipseq
updated 2.2 years ago by ★ 5.2k • written 2.2 years ago by • 0
0
votes
2
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672
views
CSAW Users Guide Ch 4-6 are not accessible/readable
csaw csawUsersGuide
updated 2.5 years ago by ★ 28k • written 2.5 years ago by • 0
0
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1
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1.6k
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[CSAW] Erreur : Negative counts not allowed
csaw
2.6 years ago Nicolas Servant ▴ 260
3
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2
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1.1k
views
csaw: when not to dedup
csaw dedup
updated 2.7 years ago by • 0 • written 8.0 years ago by • 0
3
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5
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2.5k
views
csaw for ATAC, quantitation of Tn5 insertion sites only
csaw ATAC-seq Tn5 insertions
updated 3.5 years ago by ▴ 10 • written 3.6 years ago by ▴ 50
2
votes
1
reply
1.2k
views
normOffsets in csaw
csaw
updated 3.7 years ago by ★ 28k • written 3.7 years ago by ★ 4.1k
1
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2
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1.2k
views
Error in csaw::windowCounts when using readParam
csaw GenomeInfoDb
updated 3.7 years ago by ★ 28k • written 3.7 years ago by ▴ 50
0
votes
4
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1.7k
views
DiffBind or csaw between different transcription factors
DiffBind csaw
updated 3.9 years ago by ★ 28k • written 3.9 years ago by ▴ 20
1
vote
3
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1.1k
views
csaw differential binding visualization
csaw
updated 4.1 years ago by ★ 28k • written 4.1 years ago by ▴ 140
2
votes
1
reply
954
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 ★ 4.1k
3
votes
1
reply
1.7k
views
Correct use of TMM / normalization factors based on large bins
csaw TMM
4.7 years ago ATpoint ★ 4.1k
1
vote
7
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1.7k
views
Error while running normOffsets in diffhic
diffhic csaw
updated 4.8 years ago by ★ 28k • written 4.8 years ago by • 0
6
votes
2
replies
1.5k
views
csaw: Error in path.expand(bam.file) : invalid 'path' argument
csaw software error
updated 4.9 years ago by 25k • written 4.9 years ago by ▴ 30
3
votes
7
replies
3.8k
views
DEseq2 for differential binding analysis ChIP seq
deseq2 diffbind csaw greylistchip chipseq
updated 5.4 years ago by 42k • written 5.4 years ago by • 0
0
votes
7
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1.3k
views
A problem with csaw that I don't think is a problem with csaw
csaw caught segfault
5.5 years ago sorjuelal • 0
0
votes
4
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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
1
reply
866
views
Gene set enrichment analysis with ChIP-seq data using test statistics directly
limma csaw
updated 5.7 years ago by ★ 28k • written 5.7 years ago by ▴ 110
1
vote
3
replies
1.3k
views
CSAW ready to use R script
csaw
updated 5.7 years ago by ★ 28k • written 5.7 years ago by ▴ 10
0
votes
1
reply
1.3k
views
Best csaw normalization approach for ATAC-seq data
csaw
updated 5.7 years ago by ★ 28k • written 5.7 years ago by ▴ 60
0
votes
2
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999
views
csaw: how to hack filtering windows by negative input controls?
csaw
updated 5.8 years ago by ★ 28k • written 5.8 years ago by ★ 2.0k
2
votes
5
replies
1.2k
views
Differential ChIP-seq analysis
diffbind csaw
updated 5.9 years ago by ★ 5.2k • written 5.9 years ago by • 0
0
votes
5
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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 6.0 years ago by ★ 28k • written 6.0 years ago by • 0
2
votes
2
replies
1.1k
views
csaw: Estimate fragment length
csaw
6.2 years ago nicolas.descostes ▴ 20
0
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3
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1.3k
views
csaw intallation issue: cannot find "lib" in Rhtslib installation
diffhic csaw Rhtslib
updated 6.6 years ago by 25k • written 6.6 years ago by • 0
3
votes
7
replies
2.0k
views
complex design for chip-seq analysis
chipseq csaw limma design matrix multiple factor design
updated 6.6 years ago by ★ 28k • written 6.6 years ago by ★ 1.5k
1
vote
2
replies
996
views
the Normalise function in csaw
csaw
6.6 years ago tangj ▴ 10
0
votes
2
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1.2k
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
2
votes
2
replies
1.1k
views
csaw::combineTests: Error: length(ids) == nrow(tab) is not TRUE
csaw
updated 6.7 years ago by ★ 28k • written 6.7 years ago by ▴ 40
3
votes
3
replies
1.6k
views
csaw: how does unequal sample size affect filtering filterWindows step
csaw differential binding analysis sample size independent filtering statistical power
updated 6.7 years ago by ★ 28k • written 6.7 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 6.8 years ago by ★ 7.9k • written 6.8 years ago by ▴ 10
1
vote
2
replies
1.2k
views
csaw : effect of library size on filtering of uninteresting windows
csaw
updated 7.2 years ago by ★ 28k • written 7.2 years ago by ▴ 100
2
votes
2
replies
940
views
Run windowCounts only on annotated regions?
csaw
updated 7.2 years ago by ★ 28k • written 7.2 years ago by ▴ 40
3
votes
1
reply
1.6k
views
Hill in P-value distribution for heterogenous ChIP-seq samples
csaw limma sva qsmooth edger
updated 7.3 years ago by ★ 28k • written 7.3 years ago by ▴ 70
3
votes
6
replies
1.9k
views
Differential Pol2 pausing analysis
edger csaw chipseq differential binding analysis
updated 7.3 years ago by ★ 28k • written 7.3 years ago by • 0
3
votes
3
replies
1.6k
views
Use csaw to build matrix for heatmap?
csaw chipseq edger
updated 7.3 years ago by ★ 28k • written 7.3 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 7.3 years ago by ★ 28k • written 7.3 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 7.6 years ago by ★ 28k • written 7.6 years ago by ▴ 20
2
votes
11
replies
1.9k
views
csaw autosim.R: Error in crunch2BAM(fnames): failed to sort BAM file
csaw
7.6 years ago endrebak85 ▴ 40
2
votes
2
replies
1.1k
views
csaw: removing PCR duplicates using dedup flag
csaw dedup
updated 7.6 years ago by 65k • written 7.6 years ago by • 0
2
votes
1
reply
1.9k
views
csaw with negative controls
csaw
7.8 years ago chriad ▴ 10
5
votes
6
replies
2.0k
views
Getting normalized read counts from region counts
regionCounts TMM csaw
7.9 years ago saadmurtazakhan ▴ 10
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
1
vote
3
replies
1.9k
views
csaw filterWindows function results in a warning: ("Zero library size detected.")
csaw
updated 8.0 years ago by ★ 28k • written 8.0 years ago by ▴ 10
50 results • Page 1 of 1
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Comment: error running enricher from clusterprofiler by Yael • 0
It worked!!! Thanks alot, i think something in the gene_list wasnt right... Thanks agian
Comment: Create protein sequences including variants from a VCF file by Yun • 0
This cannot work for a SNV file, since `injectSNPs` need a `SNPlocs` object
Comment: Can log2cpm be used for proteomics data normalization? by Daniel • 0
Thank you for the quick reply and I apologize for it being on the wrong thread but the "post tag" function wasn't working properly.
Comment: Error while installing BiocManager::install("org.Vdahliae.eg.db") by Patadù ▴ 10
I have arranged the code again following the other post and also the script you suggested. Now, I managed to install `org.Vdahliae.eg.db`. …
Comment: Error while installing BiocManager::install("org.Vdahliae.eg.db") by Patadù ▴ 10
Thanks again Guido, I will try to run the script you have suggested and see if I can install the package. Yes, I have seen this message a…
Votes
Answer: Trim/Filter out-of-bounds GRanges
Comment: How to correctly adjust for gender in edgeR
Create protein sequences including variants from a VCF file
A: DEXSeq design formula
Answer: SGSeq: moving toward diffex from SGSeq analysis
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