Showing : differential binding analysis • reset
1
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6
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question about DiffBind
DiffBind differential binding analysis
updated 8.6 years ago by ★ 5.2k • written 8.7 years ago by • 0
5
votes
7
replies
4.5k
views
Differential binding of ATAC-seq data with no replicates
ATAC differential binding analysis no replicates DEseq2 chromatin
7.1 years ago BioinfGuru ▴ 30
3
votes
6
replies
4.4k
views
Analyzing data without replicates using DiffBind
diffbind bioconductor differential binding analysis without replicate chipseq
6.4 years ago Hesh ▴ 10
3
votes
9
replies
3.5k
views
DiffBind BED output with score
diffbind differential binding analysis
updated 7.2 years ago by ★ 5.2k • written 7.2 years ago by ▴ 60
2
votes
10
replies
3.3k
views
DESeq2 results export padj sorted
deseq2 deseq differential binding analysis
updated 6.3 years ago by 41k • written 6.3 years ago by ▴ 60
4
votes
1
reply
2.8k
views
csaw - workflow to incorporate input/control samples?
csaw chipseq differential binding analysis
updated 8.0 years ago by ★ 28k • written 8.0 years ago by ▴ 10
4
votes
7
replies
2.6k
views
Differential ChIP-Seq Analysis with DESeq2
chipseq deseq2 featurecounts differential binding analysis
updated 5.9 years ago by 41k • written 5.9 years ago by ▴ 20
2
votes
1
reply
2.0k
views
DiffBind dba.analyze() to return all differentially enriched peaks?
diffbind p-value differential binding analysis fold enrichment values using diffbind
updated 7.9 years ago by ★ 5.2k • written 7.9 years ago by • 0
3
votes
6
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1.9k
views
Differential Pol2 pausing analysis
edger csaw chipseq differential binding analysis
updated 7.2 years ago by ★ 28k • written 7.2 years ago by • 0
2
votes
4
replies
1.8k
views
Matrix not full rank - DESeq2
deseq2 model matrix not full rank model.matrix deseq differential binding analysis
updated 6.3 years ago by ★ 3.7k • written 6.3 years ago by ▴ 60
4
votes
5
replies
1.8k
views
Multi-factor blocking in DiffBind
diffbind differential binding analysis multiple factor design
written 6.6 years ago by ▴ 30
9
votes
17
replies
1.8k
views
DESeq2 design subcategories
deseq2 deseq differential binding analysis
updated 6.4 years ago by 41k • written 6.4 years ago by ▴ 60
1
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1
reply
1.6k
views
Differential binding using csaw
csaw differential binding analysis chipseq differential expression differential gene expression
updated 8.1 years ago by ★ 28k • written 8.1 years ago by ▴ 10
3
votes
3
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1.6k
views
csaw: how does unequal sample size affect filtering filterWindows step
csaw differential binding analysis sample size independent filtering statistical power
updated 6.6 years ago by ★ 28k • written 6.6 years ago by • 0
4
votes
6
replies
1.5k
views
DESeq2 design and stats question
deseq2 differential binding analysis deseq atac-seq
updated 6.2 years ago by 41k • written 6.3 years ago by ▴ 60
1
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3
replies
1.5k
views
Is there a way to run Diffbind without the normalization ?
diffbind differential binding analysis
updated 3.5 years ago by ★ 5.2k • written 5.7 years ago by ▴ 10
4
votes
2
replies
1.4k
views
Csaw : filter windows based on matched negative control
csaw differential binding analysis
8.5 years ago Pierre-François Roux • 0
2
votes
4
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1.4k
views
DiffBind report and MA-plot DB difference
diffbind differential binding analysis R report
updated 6.3 years ago by ★ 5.2k • written 6.3 years ago by • 0
4
votes
7
replies
1.4k
views
Filtering DESeq2 result export along multiple lines
deseq2 differential binding analysis deseq
updated 6.4 years ago by 41k • written 6.4 years ago by ▴ 60
4
votes
7
replies
1.4k
views
Altering design following DESeqDataSetFromMatrix and DESeq
deseq2 differential binding analysis
updated 6.5 years ago by 41k • written 6.5 years ago by ▴ 60
3
votes
2
replies
1.4k
views
diffbind finding not differential site
diffbind chipseq histone chip-seq differential binding analysis
updated 5.5 years ago by ★ 5.2k • written 5.5 years ago by • 0
0
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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
2
votes
5
replies
1.3k
views
Mapping DESeq2 output back to chromosomal positions
deseq2 deseq diffbind differential binding analysis
updated 6.4 years ago by 41k • written 6.4 years ago by ▴ 60
2
votes
1
reply
1.3k
views
Strategy for choosing window size and read extension length for csaw?
csaw differential binding analysis bin size
updated 8.0 years ago by ★ 28k • written 8.0 years ago by ★ 7.9k
4
votes
3
replies
1.2k
views
Opinions on DESeqDataSetFromMatrix rowSums minimum for ChIP and/or ATAC-seq
deseq2 atac-seq chipseq differential binding analysis
updated 6.4 years ago by ★ 28k • written 6.4 years ago by ▴ 60
2
votes
4
replies
1.1k
views
How to judge DESeq2_block and EdgeR_block result
diffbind Deseq2 edger differential binding analysis
updated 6.4 years ago by ★ 5.2k • written 6.4 years ago by • 0
2
votes
1
reply
1.1k
views
Receiving error trying to import matrix into DESeq2
deseq2 deseq differential binding analysis
updated 6.5 years ago by ▴ 60 • written 6.5 years ago by ▴ 60
0
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3
replies
1.0k
views
DESeq2 group comparison
deseq2 deseq differential binding analysis
updated 5.6 years ago by 41k • written 5.6 years ago by ▴ 60
2
votes
2
replies
820
views
Cleaning up DiffBind counts in relation to chromosome map
diffbind chipseq differential binding analysis
updated 6.5 years ago by ★ 5.2k • written 6.5 years ago by ▴ 60
0
votes
1
reply
807
views
Diffbind: How to compare the DBs called with and without a blocking factor
diffbind differential binding analysis blocking
updated 6.3 years ago by ★ 5.2k • written 6.3 years ago by • 0
1
vote
2
replies
784
views
Pre-filtering DESeqDataSetFromMatrix input
deseq2 differential binding analysis
updated 6.5 years ago by 65k • written 6.5 years ago by ▴ 60
31 results • Page 1 of 1
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Comment: Why p value inconsistent when using different number of pathway score? by Chris • 0
Hi Robert, if two conditions don't have hundreds of differential express genes ( in some conditions such as peripheral blood Alzheimer vs n…
Answer: Dominance Index for Shotgun Metagenomics Data by Leo Lahti ▴ 40
1. Note that Simpson's dominance index (\lambda) is a different index than inverse Simpson (1/\lambda) or reciprocal Simpson (1-\lambda). T…
Comment: Math expression in shapeCustom legend in EnhancedVolcano by pl23 • 0
Thank you very much - that worked perfectly! Word of warning to those who try this: it screws up the other legends because of the markdown …
Answer: PCA plot suggestions by Michael Love 41k
For help with interpretation and design of analysis, I recommend working with a local statistician. Due to time restrictions, I can only…
Comment: DESeq2 Error in `.rowNamesDF<-`(x, value = value): Invalid 'row.names' length by ussarizona ▴ 10
Hi Michael, Yes, I could figure it out what does the error mean. In my matrix I had the first colum GeneID while in my condition I only h…
Votes
Answer: Dominance Index for Shotgun Metagenomics Data
Answer: Math expression in shapeCustom legend in EnhancedVolcano
Comment: DESeq2 Error in `.rowNamesDF<-`(x, value = value): Invalid 'row.names' length
Comment: Deseq2. decontXcounts not integers. Useful alternative?
Comment: Opposite sign of LFC in count plots of DEGs (DESeq2)
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