Showing : csaw • reset
0
votes
0
replies
640
views
Calculation of ChIP-seq normalization factors with non-conventional spike-in assumptions
csaw ChIPseq DiffBind
13 months ago jared.andrews07 ▴ 30
0
votes
0
replies
506
views
Csaw - WindowCount : Paired reads unexpectedly filtered out
windowCount csaw paired
18 months ago julie.chevalier • 0
2
votes
4
replies
1.3k
views
Error with regionCounts()
csaw
20 months ago Chris ▴ 20
0
votes
0
replies
583
views
some questions about eliminating efficiency biaes in csaw user's guide
csawUsersGuide csaw
22 months ago sashu • 0
3
votes
4
replies
2.3k
views
RiP RLE normalisation using spike-in peaks in DiffBind for ChIP-seq
DiffBind SpikeIn Normalization ChIP-seq csaw
2.0 years ago • updated 23 months ago spg • 0
0
votes
0
replies
600
views
normFactors or calcNormFactors (computing the normalization or scaling factors)
limma edgeR csaw
2.0 years ago Bogdan ▴ 670
1
vote
3
replies
2.0k
views
regionCounts() from csaw - object 'fancy_mseq' not found
ATACSeq regionCounts csaw
updated 12 months ago by • 0 • written 2.6 years ago by • 0
1
vote
2
replies
1.6k
views
Normalize ChIP-seq samples with different signal-to-noise ratio
csaw edger tmm chipseq
updated 2.8 years ago by ★ 5.2k • written 2.8 years ago by • 0
0
votes
2
replies
834
views
CSAW Users Guide Ch 4-6 are not accessible/readable
csaw csawUsersGuide
updated 3.1 years ago by ★ 28k • written 3.1 years ago by • 0
0
votes
1
reply
1.9k
views
[CSAW] Erreur : Negative counts not allowed
csaw
3.2 years ago Nicolas Servant ▴ 260
3
votes
5
replies
3.1k
views
csaw for ATAC, quantitation of Tn5 insertion sites only
csaw ATAC-seq Tn5 insertions
updated 4.2 years ago by ▴ 10 • written 4.2 years ago by ▴ 50
2
votes
1
reply
1.4k
views
normOffsets in csaw
csaw
updated 4.3 years ago by ★ 28k • written 4.3 years ago by ★ 4.6k
1
vote
2
replies
1.4k
views
Error in csaw::windowCounts when using readParam
csaw GenomeInfoDb
updated 4.3 years ago by ★ 28k • written 4.3 years ago by ▴ 50
0
votes
4
replies
2.1k
views
DiffBind or csaw between different transcription factors
DiffBind csaw
updated 4.5 years ago by ★ 28k • written 4.5 years ago by ▴ 20
1
vote
3
replies
1.4k
views
csaw differential binding visualization
csaw
updated 4.7 years ago by ★ 28k • written 4.7 years ago by ▴ 140
2
votes
1
reply
1.2k
views
Using Input Samples in ChIP-seq Differential Analysis (csaw/edgeR)
csaw chip-seq
updated 5.0 years ago by ★ 28k • written 5.0 years ago by ★ 4.6k
3
votes
1
reply
2.0k
views
Correct use of TMM / normalization factors based on large bins
csaw TMM
5.3 years ago ATpoint ★ 4.6k
1
vote
7
replies
2.0k
views
Error while running normOffsets in diffhic
diffhic csaw
updated 5.4 years ago by ★ 28k • written 5.4 years ago by • 0
6
votes
2
replies
1.8k
views
csaw: Error in path.expand(bam.file) : invalid 'path' argument
csaw software error
updated 5.5 years ago by 25k • written 5.5 years ago by ▴ 30
3
votes
7
replies
4.5k
views
DEseq2 for differential binding analysis ChIP seq
deseq2 diffbind csaw greylistchip chipseq
updated 6.0 years ago by 43k • written 6.0 years ago by • 0
0
votes
7
replies
1.6k
views
A problem with csaw that I don't think is a problem with csaw
csaw caught segfault
6.1 years ago sorjuelal • 0
0
votes
4
replies
1.8k
views
csaw spike-in normalization
ChIP-seq csaw
updated 6.1 years ago by ★ 28k • written 6.1 years ago by ▴ 260
0
votes
1
reply
1.0k
views
Gene set enrichment analysis with ChIP-seq data using test statistics directly
limma csaw
updated 6.3 years ago by ★ 28k • written 6.3 years ago by ▴ 170
1
vote
3
replies
1.6k
views
CSAW ready to use R script
csaw
updated 6.3 years ago by ★ 28k • written 6.3 years ago by ▴ 10
0
votes
1
reply
1.5k
views
Best csaw normalization approach for ATAC-seq data
csaw
updated 6.3 years ago by ★ 28k • written 6.3 years ago by ▴ 60
0
votes
2
replies
1.2k
views
csaw: how to hack filtering windows by negative input controls?
csaw
updated 6.4 years ago by ★ 28k • written 6.4 years ago by ★ 2.0k
2
votes
5
replies
1.4k
views
Differential ChIP-seq analysis
diffbind csaw
updated 6.5 years ago by ★ 5.2k • written 6.5 years ago by • 0
0
votes
5
replies
1.6k
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 6.6 years ago by ★ 28k • written 6.6 years ago by • 0
2
votes
2
replies
1.2k
views
csaw: Estimate fragment length
csaw
6.8 years ago nicolas.descostes ▴ 20
0
votes
3
replies
1.5k
views
csaw intallation issue: cannot find "lib" in Rhtslib installation
diffhic csaw Rhtslib
updated 7.2 years ago by 25k • written 7.2 years ago by • 0
3
votes
7
replies
2.4k
views
complex design for chip-seq analysis
chipseq csaw limma design matrix multiple factor design
updated 7.2 years ago by ★ 28k • written 7.2 years ago by ★ 1.5k
1
vote
2
replies
1.1k
views
the Normalise function in csaw
csaw
7.2 years ago tangj ▴ 10
0
votes
2
replies
1.4k
views
Differential ChIP-seq with csaw: How to normalise counts on repetitive regions (telomers)?
csaw histone chip-seq chip-seq
updated 7.3 years ago by ★ 28k • written 7.3 years ago by • 0
2
votes
2
replies
1.3k
views
csaw::combineTests: Error: length(ids) == nrow(tab) is not TRUE
csaw
updated 7.3 years ago by ★ 28k • written 7.3 years ago by ▴ 40
3
votes
3
replies
1.8k
views
csaw: how does unequal sample size affect filtering filterWindows step
csaw differential binding analysis sample size independent filtering statistical power
updated 7.3 years ago by ★ 28k • written 7.3 years ago by • 0
3
votes
11
replies
2.6k
views
Exporting normalized counts over final DB windows from csaw
csaw edger chip-seq
updated 7.4 years ago by ★ 7.9k • written 7.4 years ago by ▴ 10
1
vote
2
replies
1.4k
views
csaw : effect of library size on filtering of uninteresting windows
csaw
updated 7.8 years ago by ★ 28k • written 7.8 years ago by ▴ 100
2
votes
2
replies
1.1k
views
Run windowCounts only on annotated regions?
csaw
updated 7.8 years ago by ★ 28k • written 7.8 years ago by ▴ 40
3
votes
1
reply
1.7k
views
Hill in P-value distribution for heterogenous ChIP-seq samples
csaw limma sva qsmooth edger
updated 7.9 years ago by ★ 28k • written 7.9 years ago by ▴ 70
3
votes
6
replies
2.2k
views
Differential Pol2 pausing analysis
edger csaw chipseq differential binding analysis
updated 7.9 years ago by ★ 28k • written 7.9 years ago by • 0
3
votes
3
replies
1.8k
views
Use csaw to build matrix for heatmap?
csaw chipseq edger
updated 7.9 years ago by ★ 28k • written 7.9 years ago by • 0
3
votes
4
replies
2.2k
views
Interpretation of cross correlation plot to determine fragment length
csaw chip-seq histone
updated 7.9 years ago by ★ 28k • written 7.9 years ago by • 0
4
votes
2
replies
2.6k
views
Removing GC content bias and trended bias from ChIP-seq data
csaw chip-seq normalization edger cqn
updated 8.2 years ago by ★ 28k • written 8.2 years ago by ▴ 20
2
votes
11
replies
2.1k
views
csaw autosim.R: Error in crunch2BAM(fnames): failed to sort BAM file
csaw
8.2 years ago endrebak85 ▴ 40
2
votes
2
replies
1.3k
views
csaw: removing PCR duplicates using dedup flag
csaw dedup
updated 8.2 years ago by 67k • written 8.2 years ago by • 0
2
votes
1
reply
2.1k
views
csaw with negative controls
csaw
8.5 years ago • updated 8.4 years ago chriad ▴ 10
5
votes
6
replies
2.3k
views
Getting normalized read counts from region counts
regionCounts TMM csaw
8.5 years ago saadmurtazakhan ▴ 10
1
vote
18
replies
3.7k
views
Normalization of chip-seq data in manually specified regions using CSAW
chip-seq TSS TMM csaw
updated 8.6 years ago by ★ 28k • written 8.6 years ago by ▴ 10
1
vote
3
replies
2.0k
views
csaw filterWindows function results in a warning: ("Zero library size detected.")
csaw
updated 8.6 years ago by ★ 28k • written 8.6 years ago by ▴ 10
3
votes
1
reply
1.5k
views
window counts in csaw
csaw counts
updated 8.6 years ago by ★ 28k • written 8.6 years ago by • 0
50 results • Page 1 of 1
Recent ...
Replies
Comment: Cross-validation with multiple control subgroups in limma by Ali Barry ▴ 40
Thanks so much for taking the time here, the insights are much appreciated. I suspected I'd have to ad hoc compare results if I did repeat …
Answer: Cross-validation with multiple control subgroups in limma by Gordon Smyth 52k
limma doesn't do cross-validation or resampling. Like most classical linear modeling procedures in statistics, limma uses a statistical mod…
Comment: Issues with seqlevelsStyle when making custom txdb objects for genomes/annotatio by Robert Castelo ★ 3.4k
Hi Hervé, thank you very much for your input into how to properly build and manage TxDb objects. gDNAx has two main inputs, one or more BAM…
Comment: Biostrings: Error writing long reads (>200 kbps) with writeQualityScaledXStringS by Aidan ▴ 60
Quick update: this is fixed in a branch awaiting PR to Biostrings (https://github.com/Bioconductor/Biostrings/pull/122). Should be in `deve…
Answer: Can DESeq2's design compensate for sequencing experimental design shortcomings? by Michael Love 43k
For statistical analysis plans, I recommend working with a local statistician or someone familiar with linear models in R. I have to reserv…
Votes
Comment: Issues with seqlevelsStyle when making custom txdb objects for genomes/annotatio
C: edgeR and lack of counts ID on CPM matrix
A: DESeq2 Following RSEM
A: importing RSEM data into DESeq2
A: Expected counts from RSEM in DESeq2
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