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ChIP-seq heatmap: Which MACS2 output file should we give as input into deeptools computeMatrix?
deeptools computeMatrix RNA-Seq ChIP-Seq MACS2
6.1 years ago by salamandra ▴ 550
0
votes
2
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1.9k
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MACS2: What is in 4th column of treat_pvalue.bdg/treat_qvalue.bdg files?
ChIP-Seq MACS2
2.4 years ago by salamandra ▴ 550
5
votes
14
replies
2.8k
views
Files to compare ChIP vs Input on genome browser: after alignment or peak calling?
ChIP-seq genome browser MACS2
updated 6.1 years ago by 8.9k • written 6.1 years ago by ▴ 550
5
votes
5
replies
1.4k
views
Wig file interpreted as bed file in genome browser
Genome Browser
updated 6.1 years ago by ▴ 580 • written 6.1 years ago by ▴ 550
5
votes
6
replies
9.0k
views
Visualize bigwig, bedgraph, wig files on Genome Browser?
RNA-Seq ChIP-Seq Genome Browser
updated 6.1 years ago by ★ 2.4k • written 6.1 years ago by ▴ 550
4
votes
8
replies
1.6k
views
ChIP-seq: When trimming Input samples should we also trim ChIP samples?
ChIP-Seq QC
6.2 years ago by salamandra ▴ 550
3
votes
4
replies
2.4k
views
ChIP-seq: Should we be consistent with the control used (IgG/Input) among different conditions?
ChIP-Seq Controls
updated 6.2 years ago by 104k • written 6.2 years ago by ▴ 550
1
vote
3
replies
3.9k
views
FastQC report: Why no error in 'Adapter content' and which sequences of 'Overrepresented sequences' should trim?
sequencing RNA-Seq ChIP-Seq
6.2 years ago by salamandra ▴ 550
13
votes
12
replies
7.7k
views
6 follow
TopHat installation error
tophat
updated 6.3 years ago by ▴ 60 • written 7.0 years ago by ▴ 550
0
votes
0
replies
1.4k
views
Transcription factors and closed/activated/repressed chromatin
ChIP-Seq chromatin ATAC-seq
6.3 years ago by salamandra ▴ 550
1
vote
1
reply
1.4k
views
ChIP-seq: Why MACS doesn't apply tag shifting to the control sample?
ChIP-Seq
updated 6.4 years ago by ▴ 50 • written 6.4 years ago by ▴ 550
7
votes
6
replies
3.6k
views
MACS for chip-seq: difference between sonication size(bandwidth) and fragment size?
ChIP-Seq MACS
updated 6.4 years ago by 81k • written 6.4 years ago by ▴ 550
16
votes
5
replies
12k
views
Install DESeq2 and edgeR with Anaconda
Anaconda DESeq2 edgeR
updated 6.5 years ago by ▴ 80 • written 6.9 years ago by ▴ 550
1
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2
replies
1.8k
views
list in which each element is a vector of GO BP ids corresponding to an entrez gene
R org.Hs.eg.db lapply
updated 6.6 years ago by 20 • written 6.8 years ago by ▴ 550
2
votes
2
replies
4.5k
views
End coordinate bigger than chromosome size converting bedgraph to bigwig/ Setting macs2 chromosome size
ChIP-Seq
updated 6.6 years ago by ★ 16k • written 6.7 years ago by ▴ 550
0
votes
0
replies
1.7k
views
GOHyperGParams GOstats R package - categorySubsetIds parameter
p-value Hypergeometric test R GOstats
6.8 years ago by salamandra ▴ 550
0
votes
1
reply
2.8k
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Enrichment heatmap - GOstats package of R
R GOstats p-value
6.8 years ago by salamandra ▴ 550
2
votes
2
replies
1.6k
views
MACS2 bdgpeakcall gives UnboundLocalError: local variable 'peak_content' referenced before assignment:
ChIP-Seq MACS2
6.8 years ago by salamandra ▴ 550
2
votes
2
replies
1.2k
views
all the peaks of MACS2 BED file starting at position 0
MACS2
6.8 years ago by salamandra ▴ 550
4
votes
5
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4.7k
views
Which peaks in the bed file output by MACS2 are significant ?
MACS2.0 Homer annotatePeaks.pl
updated 6.9 years ago by 104k • written 6.9 years ago by ▴ 550
4
votes
3
replies
1.5k
views
Retrieve header of column (field) in which data is above or equals a number
Commandline awk
updated 6.9 years ago by 161k • written 6.9 years ago by ▴ 550
2
votes
6
replies
39k
views
Export graph in R - error QuartzBitmap_Output - unable to open file
R
7.0 years ago by salamandra ▴ 550
2
votes
2
replies
1.7k
views
Can't open help page R studio with hit tab when start writing the name of a function + F1
R RStudio
updated 7.0 years ago by 11k • written 7.0 years ago by ▴ 550
1
vote
13
replies
5.5k
views
Chip-seq - fastqc: zip file doesn't open
ChIP-Seq FastQC
7.4 years ago by salamandra ▴ 550
1
vote
4
replies
2.7k
views
Remove/Identify deprecated IDs from a list of Entrez IDs programatically
entrez
updated 17 months ago by 43k • written 8.8 years ago by ▴ 550
1
vote
2
replies
2.4k
views
Remove/Identify pseudogenes from a list of Entrez IDs programatically
entrez pseudogenes
updated 17 months ago by 43k • written 8.8 years ago by ▴ 550
76 results • Page 2 of 2
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