Showing : differential binding analysis • reset
4
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5
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2.1k
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Multi-factor blocking in DiffBind
diffbind differential binding analysis multiple factor design
written 7.2 years ago by ▴ 30
1
vote
3
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1.8k
views
Is there a way to run Diffbind without the normalization ?
diffbind differential binding analysis
updated 4.2 years ago by ★ 5.2k • written 6.4 years ago by ▴ 10
3
votes
2
replies
1.6k
views
diffbind finding not differential site
diffbind chipseq histone chip-seq differential binding analysis
updated 6.2 years ago by ★ 5.2k • written 6.2 years ago by • 0
0
votes
3
replies
1.2k
views
DESeq2 group comparison
deseq2 deseq differential binding analysis
updated 6.3 years ago by 43k • written 6.3 years ago by ▴ 60
4
votes
7
replies
3.0k
views
Differential ChIP-Seq Analysis with DESeq2
chipseq deseq2 featurecounts differential binding analysis
updated 6.6 years ago by 43k • written 6.6 years ago by ▴ 20
4
votes
6
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1.8k
views
DESeq2 design and stats question
deseq2 differential binding analysis deseq atac-seq
updated 6.9 years ago by 43k • written 6.9 years ago by ▴ 60
0
votes
1
reply
969
views
Diffbind: How to compare the DBs called with and without a blocking factor
diffbind differential binding analysis blocking
updated 7.0 years ago by ★ 5.2k • written 7.0 years ago by • 0
2
votes
4
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1.7k
views
DiffBind report and MA-plot DB difference
diffbind differential binding analysis R report
updated 7.0 years ago by ★ 5.2k • written 7.0 years ago by • 0
2
votes
10
replies
4.0k
views
DESeq2 results export padj sorted
deseq2 deseq differential binding analysis
updated 7.0 years ago by 43k • written 7.0 years ago by ▴ 60
2
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4
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2.3k
views
Matrix not full rank - DESeq2
deseq2 model matrix not full rank model.matrix deseq differential binding analysis
updated 7.0 years ago by ★ 3.8k • written 7.0 years ago by ▴ 60
2
votes
5
replies
1.5k
views
Mapping DESeq2 output back to chromosomal positions
deseq2 deseq diffbind differential binding analysis
updated 7.0 years ago by 43k • written 7.0 years ago by ▴ 60
2
votes
4
replies
1.3k
views
How to judge DESeq2_block and EdgeR_block result
diffbind Deseq2 edger differential binding analysis
updated 7.0 years ago by ★ 5.2k • written 7.0 years ago by • 0
4
votes
3
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1.4k
views
Opinions on DESeqDataSetFromMatrix rowSums minimum for ChIP and/or ATAC-seq
deseq2 atac-seq chipseq differential binding analysis
updated 7.0 years ago by ★ 28k • written 7.0 years ago by ▴ 60
9
votes
17
replies
2.1k
views
DESeq2 design subcategories
deseq2 deseq differential binding analysis
updated 7.1 years ago by 43k • written 7.1 years ago by ▴ 60
5
votes
6
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5.3k
views
Analyzing data without replicates using DiffBind
diffbind bioconductor differential binding analysis without replicate chipseq
7.1 years ago Hesh ▴ 10
4
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7
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1.7k
views
Filtering DESeq2 result export along multiple lines
deseq2 differential binding analysis deseq
updated 7.1 years ago by 43k • written 7.1 years ago by ▴ 60
2
votes
2
replies
935
views
Cleaning up DiffBind counts in relation to chromosome map
diffbind chipseq differential binding analysis
updated 7.1 years ago by ★ 5.2k • written 7.1 years ago by ▴ 60
4
votes
7
replies
1.6k
views
Altering design following DESeqDataSetFromMatrix and DESeq
deseq2 differential binding analysis
updated 7.1 years ago by 43k • written 7.1 years ago by ▴ 60
1
vote
2
replies
903
views
Pre-filtering DESeqDataSetFromMatrix input
deseq2 differential binding analysis
updated 7.2 years ago by 67k • written 7.2 years ago by ▴ 60
2
votes
1
reply
1.2k
views
Receiving error trying to import matrix into DESeq2
deseq2 deseq differential binding analysis
updated 7.2 years ago by ▴ 60 • written 7.2 years ago by ▴ 60
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
5
votes
7
replies
5.0k
views
Differential binding of ATAC-seq data with no replicates
ATAC differential binding analysis no replicates DEseq2 chromatin
7.8 years ago BioinfGuru ▴ 70
3
votes
9
replies
4.2k
views
DiffBind BED output with score
diffbind differential binding analysis
updated 7.9 years ago by ★ 5.2k • written 7.9 years ago by ▴ 60
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
0
votes
3
replies
1.6k
views
Chip-seq analysis with input
chip-seq differential binding analysis
updated 8.4 years ago by ★ 28k • written 8.4 years ago by • 0
2
votes
1
reply
2.3k
views
DiffBind dba.analyze() to return all differentially enriched peaks?
diffbind p-value differential binding analysis fold enrichment values using diffbind
updated 8.5 years ago by ★ 5.2k • written 8.6 years ago by • 0
4
votes
1
reply
3.1k
views
csaw - workflow to incorporate input/control samples?
csaw chipseq differential binding analysis
updated 8.7 years ago by ★ 28k • written 8.7 years ago by ▴ 10
2
votes
1
reply
1.5k
views
Strategy for choosing window size and read extension length for csaw?
csaw differential binding analysis bin size
updated 8.7 years ago by ★ 28k • written 8.7 years ago by ★ 7.9k
1
vote
1
reply
1.8k
views
Differential binding using csaw
csaw differential binding analysis chipseq differential expression differential gene expression
updated 8.7 years ago by ★ 28k • written 8.7 years ago by ▴ 10
4
votes
2
replies
1.6k
views
Csaw : filter windows based on matched negative control
csaw differential binding analysis
9.2 years ago Pierre-François Roux • 0
1
vote
6
replies
6.2k
views
question about DiffBind
DiffBind differential binding analysis
updated 9.3 years ago by ★ 5.2k • written 9.4 years ago by • 0
31 results • Page 1 of 1
Recent ...
Replies
Answer: Incorporating Salmon offset matrix into Wilcoxon DEG analysis by Gordon Smyth 52k
To compute CPM values from edgeR: ``` y <- DGEList(counts = counts, samples = samples, genes = genes, group = samples$Disease_status) y <- …
Comment: edgeR + tximport: calcNormFactors and the usage of offsets by Gordon Smyth 52k
Follow the vignette. It explains how to call edgeR's cpm function to use the offsets.
Comment: edgeR + tximport: calcNormFactors and the usage of offsets by Andre • 0
But if i want to do another type of analysis like Wilcoxon/Mann-Whitney and want to incorporate salmon offset can i simply use the cpm func…
Comment: DESeq error: counts matrix should be numeric, currently it has mode: character by Kucsera • 0
After applying your suggestion, the following error pops up: ``` Error in mde(x) : 'list' object cannot be coerced to type 'double' ```
Answer: DESeq error: counts matrix should be numeric, currently it has mode: character by ATpoint ★ 4.6k
R thinks your data are characters (e.g. "1", "2", instead of 1, 2) so given that your `counts_data` indeed only contains counts, do: `mo…
Votes
A: GWAS analysis with Illumina HumanOmni5-4 BeadChip - recommended software and wor
A: GWAS analysis with Illumina HumanOmni5-4 BeadChip - recommended software and wor
A: RNA-seq Normalisation - normalise all samples in experiment or only the ones use
Answer: Can DESeq2's design compensate for sequencing experimental design shortcomings?
Comment: Issues with seqlevelsStyle when making custom txdb objects for genomes/annotatio
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