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73 results • Page
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Showing :
deepTools
•
reset
0
Votes
8
Replies
2.9k
Views
Overlapping regions in a BedGraph file
bedgraph
GRO-Seq
ChIP-Seq
deeptools
5.0 years ago
Sam
• 70
• updated 19 months ago
Simply Bioinformatics
• 150
5
Votes
10
Replies
181
Views
.sra to bam conversion results in a "< myfile > does not have BAM or CRAM format error"
SRA-toolkit
samtools
deeptools
19 months ago
jordi.planells
• 70
• updated 19 months ago
genomax
68k
5
Votes
5
Replies
220
Views
Issue running deeptools on cluster via snakemake
Deeptools
Snakemake
20 months ago
camerond
• 70
• updated 20 months ago
russhh
♦ 4.4k
1
Vote
3
Replies
258
Views
Deeptools for ChIP-Seq
ChIP-Seq
Deeptools
Heatmap
20 months ago
yugen30
• 10
2
Votes
6
Replies
1.0k
Views
show the names of the genes on the Y axis on the heatmap Deeptools
RNA-Seq
ChIP-Seq
deepTools
4.3 years ago
Bioiris
• 0
• updated 20 months ago
yugen30
• 10
0
Votes
4
Replies
247
Views
Chip Seq analysis for H3K27me3,H3K27ac and K4me1 enrichment
ChIP-Seq
deeptools
21 months ago
Researcher
• 30
• updated 21 months ago
jared.andrews07
♦ 2.4k
1
Vote
5
Replies
761
Views
[ChIP-seq. signal plot] How to align the based line of different samples?
deepTools
ChIP-seq
normalization
3.0 years ago
chiefcat
• 100
• updated 21 months ago
Biostar
20
0
Votes
2
Replies
157
Views
bamCompare the result if 0
ChIP-Seq
deeptools
bamcompare
22 months ago
HI
• 0
• updated 22 months ago
Devon Ryan
90k
8
Votes
8
Replies
328
Views
How extract the longest overlap?
bedtools
deeptools
overlap
intersect
bedops
22 months ago
star
• 150
• updated 22 months ago
Biostar
20
2
Votes
1
Reply
170
Views
what is difference between -i and -ibam in genomCoverage?
bedtools
deeptools
bamCoverage
genomeCoverage
22 months ago
star
• 150
• updated 22 months ago
ATpoint
17k
0
Votes
2
Replies
364
Views
ChIP-Seq density plot of the TSS regions?
ChIP-Seq
Deeptools
Bedtools
IGV
ASE
23 months ago
Susmita Mandal
• 40
• updated 23 months ago
i.sudbery
4.7k
3
Votes
14
Replies
361
Views
error while reading bigwig files in computeMatrix (deeptools)
deeptools
computeMatrix
bigwig
coverage
24 months ago
Lila M
• 470
• updated 24 months ago
Devon Ryan
90k
2
Votes
4
Replies
299
Views
Identify genes with chip signal > input prior to peak calling
ChIP-Seq
enrichment
chip signal
galaxy
deeptools
24 months ago
SciDuck
• 20
0
Votes
0
Replies
154
Views
How to deal with wig files separate bu watson and crick strand
wig
GROseq
TSSprofile
deepTools
2.0 years ago
Lila M
• 470
0
Votes
5
Replies
265
Views
Deeptool ComputeGCBias causes fatal error
deeptools
computegcbias
software error
sequencing
2.1 years ago
mfro1505
• 0
• updated 2.1 years ago
RamRS
21k
2
Votes
6
Replies
480
Views
Installing and running pyGenomeTracks
pyGenomeTracks
deeptools
hicmatrix
hicexplorer
2.3 years ago
rbronste
• 240
• updated 2.1 years ago
wolffj.bioinf
• 10
3
Votes
1
Reply
338
Views
Using FeatureCounts for ChIP-seq normalised files?
deeptools
ChIP-Seq
2.1 years ago
a.rex
• 190
• updated 2.1 years ago
Devon Ryan
90k
0
Votes
0
Replies
256
Views
Can I use deeptools to calculate nucleosome positions?
deeptools
atac
2.1 years ago
a.rex
• 190
0
Votes
4
Replies
410
Views
Explaining PCA plots made from BigWig coverage files in DeepTools
deeptools
atac-seq
2.2 years ago
a.rex
• 190
• updated 2.2 years ago
RamRS
21k
0
Votes
1
Reply
210
Views
Deeptools plotCorrelation function bug?
deeptools
plotCorrelation
2.2 years ago
Zee_S
• 30
3
Votes
8
Replies
1.9k
Views
ValueError: invalid literal for int() with base 10: 'start' computeMatrix of deeptools
ChIP-Seq
Deeptools
3.6 years ago
salamandra
• 200
• updated 2.3 years ago
RamRS
21k
1
Vote
6
Replies
485
Views
deepTools2: compute matrix error
software error
deepTools
galaxy
2.4 years ago
dabates06
• 0
• updated 2.4 years ago
Devon Ryan
90k
2
Votes
2
Replies
245
Views
what scale does multiBigwigSummary use for score
multiBigwigSummary
deepTools
score
2.4 years ago
Lila M
• 470
• updated 2.4 years ago
Devon Ryan
90k
3
Votes
5
Replies
736
Views
Different bigwig file sizes between BedgraphToBigwig and bamCoverage
ucsc
bigwig
BedgraphToBigWig
bamCoverage
deeptools
2.4 years ago
m93
• 150
2
Votes
3
Replies
713
Views
deeptools bamcompare/bamcoverage merging bins?
deeptools
ChIP-Seq
2.5 years ago
gewa
• 0
• updated 2.5 years ago
ATpoint
17k
2
Votes
2
Replies
426
Views
deepTools - change line colors in profile plots above a heatmap
deeptools
profile plot
heatmap
2.5 years ago
mbk0asis
• 420
• updated 2.5 years ago
Devon Ryan
90k
2
Votes
5
Replies
851
Views
Deeptools plotHeatmap: too much black! missing data assigned incorrectly
deeptools
plotheatmap
missing data
computeMatrix
2.6 years ago
David K
• 0
• updated 2.6 years ago
Devon Ryan
90k
5
Votes
4
Replies
505
Views
deepTools plot profile problem
deepTools
profile
title
2.6 years ago
elisheva
• 70
• updated 2.6 years ago
Devon Ryan
90k
2
Votes
3
Replies
637
Views
Y axis PlotHeatMap Deeptools
Deeptools
2.6 years ago
fusion.slope
• 200
• updated 2.6 years ago
Devon Ryan
90k
1
Vote
1
Reply
477
Views
Plotting multiple signal files against a single genomic region
RNA-Seq
ChIP-Seq
deeptools
2.8 years ago
keller.mckowen
• 10
• updated 2.7 years ago
Alex Reynolds
28k
1
Vote
3
Replies
575
Views
Can't upgrade deeptools 2.5.7 to 3.0 via conda 4.5.0 on Debian Jessie
DEEPTOOLS
2.8 years ago
ZheFrench
• 220
• updated 2.8 years ago
Devon Ryan
90k
1
Vote
4
Replies
1.1k
Views
Deeptools - ComputeMatrix: Why does 'referencePoint center' gives the same heatmap as 'referencePoint TSS'
ChIP-Seq
sequencing
deeptools
2.9 years ago
salamandra
• 200
0
Votes
0
Replies
843
Views
ChIP-seq heatmap: Which MACS2 output file should we give as input into deeptools computeMatrix?
deeptools
computeMatrix
RNA-Seq
ChIP-Seq
MACS2
2.9 years ago
salamandra
• 200
2
Votes
1
Reply
681
Views
Comparison of bamCoverage log2 ratios in deeptools
deeptools
ChIP-Seq
Correlation
2.9 years ago
ATpoint
17k
• updated 2.9 years ago
Devon Ryan
90k
0
Votes
0
Replies
438
Views
Estimate Fragment Size from Single End ChipSeq with (pysam, htseq lib or deeptools API)
deeptools
pysam
HTSEQ
3.0 years ago
ZheFrench
• 220
103
Votes
43
Replies
23k
Views
17 follow
Forum:
Visualization of ChIP-seq data using Heatmaps (Updated: 06/10/16)
ChIP-Seq
visualization
deeptools
ngsplot
homer
Forum
4.9 years ago
Sinji
♦ 2.8k
• updated 3.0 years ago
chiefcat
• 100
2
Votes
3
Replies
1.2k
Views
[ChIP-seq. signal plot] How to merge ChIP-seq. biological replicates for signal profile plotting?
deepTools
ChIP-Seq
biological replicates
3.0 years ago
chiefcat
• 100
• updated 3.0 years ago
Devon Ryan
90k
3
Votes
2
Replies
1.3k
Views
Help with DeepTools
ChIP-Seq
software error
deeptools
3.1 years ago
landrjos
• 10
• updated 3.1 years ago
genomax
68k
2
Votes
2
Replies
523
Views
how to draw two different Y-axes with deeptools?
deeptools
CHH
Methylation
3.1 years ago
edoardobertolini
• 0
• updated 3.1 years ago
Devon Ryan
90k
0
Votes
5
Replies
1.4k
Views
plotProfile (deepTools) generated a peak on gene body region
deepTools
plotProfile
3.1 years ago
mbk0asis
• 420
• updated 3.1 years ago
Devon Ryan
90k
6
Votes
4
Replies
1.1k
Views
deeptools PCA vs ChIPQC PCA
deeptools
ChIPQC
Diffbind
chipseq
3.4 years ago
ZheFrench
• 220
• updated 3.4 years ago
Devon Ryan
90k
1
Vote
6
Replies
1.5k
Views
how to process spike-in with bamCoverage and plotHeatmap (with deeptools)
ChIP-Seq
spike
deeptools
normalization
3.4 years ago
alessandro.pastore
• 30
3
Votes
6
Replies
810
Views
deepTools draw coverage for specific region
alignment
bam
deepTools
3.5 years ago
Medhat
8.3k
• updated 3.5 years ago
Devon Ryan
90k
2
Votes
6
Replies
1.1k
Views
Extract further information from deepTools plotPCA
ChIP-Seq
deepTools
3.5 years ago
Roman Hillje
• 30
1
Vote
2
Replies
930
Views
plotProfile with mean of bigwig files
deeptools
plotprofile
bigwig
mean
average
3.5 years ago
ildem
• 40
3
Votes
1
Reply
662
Views
deepTools - plotHeatmap, move colorbar to the bottom
deepTools
heatmap
3.6 years ago
rbronste
• 240
• updated 3.6 years ago
Devon Ryan
90k
4
Votes
5
Replies
607
Views
Filter for regions containing large stretches of missing data
deeptools
computematrix
plotheatmap
missing data
3.6 years ago
mmmmcandrew
• 60
• updated 3.6 years ago
Alex Reynolds
28k
0
Votes
2
Replies
1.3k
Views
deeptools installation on MacBook
deeptools
mac
install
3.8 years ago
BioDH
• 0
• updated 3.6 years ago
inowkeren
• 0
5
Votes
5
Replies
985
Views
Deeptools Sorting for score values
Deeptools
Heatmaps
Sorting
3.7 years ago
groupelmarwolf
• 0
• updated 3.7 years ago
Devon Ryan
90k
2
Votes
2
Replies
1.0k
Views
bamCompare log2 ratio p-value
bamcompare
p-value
log2ratio
deepTools
3.7 years ago
dovi
• 60
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