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ATACSeqQC
•
reset
1
vote
11
replies
2.3k
views
ATAC-QC shiftGAlignmentsList function
ATAC-seq
ATACseqQC
updated 4.8 years ago by
Julie Zhu
★ 4.3k • written 4.8 years ago by
Shuang He
• 0
0
votes
9
replies
3.5k
views
No peak corresponding to the nucleosome-free regions is observed in Fragment size distribution of ATAC-seq
ATACseqQC
Fragmentsizedistribution
ATAC-seq
3.0 years ago
Xiaojie Cheng
• 0
2
votes
5
replies
1.5k
views
The meaning of results produced by the bamQC function implemented in the ATACseqQC
ATACseqQC
bamQC
ATAC-Seq
totalQNAMEs
MAPQ
updated 5.2 years ago by
Julie Zhu
★ 4.3k • written 5.2 years ago by
Gary
▴ 20
1
vote
2
replies
9.3k
views
Interpreting TSS Enrichment Score Summary
atacseq
atacseqqc
tss
enrichment
updated 3.7 years ago by
Ou, Jianhong
★ 1.3k • written 3.7 years ago by
Arpi Beshlikyan
• 0
0
votes
7
replies
2.2k
views
ATACseqQC memory overflow issue
atac-seq
software error
atacseqqc
updated 6.2 years ago by
Haibo.Liu
• 0 • written 6.2 years ago by
José Luis Lavín
▴ 10
5
votes
9
replies
3.8k
views
mm10 phastCons data for use with ATACseqQC
ATACseqQC
bsgenome
phastcons
rtracklayer
updated 7.0 years ago by
Ou, Jianhong
★ 1.3k • written 7.0 years ago by
crysis405
▴ 10
0
votes
9
replies
1.5k
views
use factorFootprints function in ATACseqQC to get DNA footprinting for certain gene region
ATACseqQC
updated 5.8 years ago by
Julie Zhu
★ 4.3k • written 5.8 years ago by
aimin.at.work
▴ 10
0
votes
2
replies
1.1k
views
ATACseqQC needs too much memory
ATACseqQC
updated 6.4 years ago by
Julie Zhu
★ 4.3k • written 6.4 years ago by
mdurante14
• 0
0
votes
5
replies
1.7k
views
ATACseqQC installation fails at shiny step
ATACseqQC
updated 4.7 years ago by
James W. MacDonald
65k • written 4.7 years ago by
kesarwani.anil
• 0
0
votes
1
reply
1.7k
views
Issue installing packages ATACseqQC and GO.db
GO.db
biocinstaller
package installation
atacseqqc
updated 6.1 years ago by
Ou, Jianhong
★ 1.3k • written 6.1 years ago by
n.pantelireis16
• 0
0
votes
1
reply
913
views
ATACseqQC questions in R language
atacseqqc
updated 5.9 years ago by
Ou, Jianhong
★ 1.3k • written 5.9 years ago by
rsong
• 0
0
votes
1
reply
1.0k
views
ATACseqQC: a few questions
ATACseqQC
updated 5.9 years ago by
Julie Zhu
★ 4.3k • written 5.9 years ago by
david.mckinnon
• 0
0
votes
3
replies
1.0k
views
Compare the DNA footprinting between different samples when using ATACseqQC
atacseqqc
updated 5.8 years ago by
Ou, Jianhong
★ 1.3k • written 5.8 years ago by
aimin.at.work
▴ 10
11
votes
21
replies
5.0k
views
How about our ATAC-Seq data quality analyzed by ATACseqQC
ATACseqQC
ATAC-Seq
quality analysis
fragment size distribution
library complexity
updated 5.2 years ago by
Julie Zhu
★ 4.3k • written 5.2 years ago by
Gary
▴ 20
0
votes
6
replies
1.9k
views
atacseqQC error while splittin the bamfile
ATACseqQC
ATAC-seq
error
split bam file
updated 5.0 years ago by
contact
• 0 • written 5.0 years ago by
Theo
▴ 10
0
votes
1
reply
977
views
ATAC-QC fragSizeDist function
ATAC-seq
ATACseqQC
updated 4.8 years ago by
Julie Zhu
★ 4.3k • written 4.8 years ago by
Shuang He
• 0
0
votes
7
replies
1.6k
views
ATACseqQC splitGAlignmentsByCut: strand values must be in '+' '-' '*'
ATACseqQC
R
updated 4.8 years ago by
Julie Zhu
★ 4.3k • written 4.8 years ago by
mbasam
• 0
0
votes
2
replies
989
views
factorFootprints, bindingSites and Profile.segmentation
ATACSeqQC
factorFootprints
updated 4.8 years ago by
Julie Zhu
★ 4.3k • written 4.8 years ago by
Nick Gomez
• 0
0
votes
4
replies
1.9k
views
ATACseqQC R package for QC scores (TSS, FRIP, NFR, IDR)
ATACseqQC
atacseq
R
updated 3.7 years ago by
Ou, Jianhong
★ 1.3k • written 3.7 years ago by
achaillon
• 0
1
vote
4
replies
1.2k
views
How to use a fimo BED output as GRanges object in factorFootprints from ATACseqQC
ATACseqQC
updated 3.7 years ago by
Julie Zhu
★ 4.3k • written 3.7 years ago by
pedro.rotcha
▴ 10
0
votes
2
replies
1.4k
views
*** caught segfault *** address 0xffffffff9a378e20, cause 'memory not mapped'
ATACseqQC
2.9 years ago
Nolan
• 0
0
votes
7
replies
661
views
ATACseqQC shiftGAlignmentsList() problem
ATACseqQC
ATACSeq
updated 9 weeks ago by
danalvoronov
▴ 10 • written 5 months ago by
jfmay
• 0
1
vote
1
reply
185
views
Error with BSgenome, wanting to analyse non-model species with ATACseqQC
ATACseqQC
updated 8 weeks ago by
James W. MacDonald
65k • written 8 weeks ago by
ronin
• 0
1
vote
7
replies
1.4k
views
TSSEscore function in ATACseqQC package
ATACseqQC
2.3 years ago
Liu Yu-Yu
• 0
0
votes
0
replies
587
views
[ATACseqQC] NA values in sigs makes heatmap not completed
ATACseqQC
ATACSeq
2.1 years ago
hyjforesight
• 0
0
votes
0
replies
780
views
Enough cell number or not based on library complexity evaluation by ATACseqQC?
ATACseqQC
ATAC-Seq
Library complexity
estimateLibComplexity
5.1 years ago
Gary
▴ 20
0
votes
0
replies
117
views
Issue with shiftGAlignmentsList() in ATACseqQC after updating
R
ATACseqQC
9 weeks ago
danalvoronov
▴ 10
0
votes
0
replies
487
views
NAs in TSSE for certain windows
ATACseqQC
2.7 years ago
red_bricks
▴ 50
0
votes
7
replies
1.8k
views
ATACseqQC shiftGAlignmentsList leads to (all(elementNROWS)>3) is not TRUE error
ATACseqQC
ATAC
ATACseq
software error
Tutorial
updated 4.9 years ago by
Steve Lianoglou
★ 13k • written 4.9 years ago by
mbasam
• 0
0
votes
1
reply
567
views
Error in ATACseqQC bamQC analysis
ATACSeq
ATACseqQC
updated 16 months ago by
Ou, Jianhong
★ 1.3k • written 16 months ago by
tahir.msajid
• 0
0
votes
0
replies
459
views
ATACseqQC function fragSizeDist returns error
fragSizeDist
ATACseqQC
2.7 years ago
xuyao15927402897
• 0
0
votes
5
replies
1.4k
views
ATACSeqQC - error when splitting files using mm10
atacseqqc
atac-seq
R
bioconductor
rsamtools
updated 4.0 years ago by
Kevin Blighe
★ 3.9k • written 4.0 years ago by
rita.monteiro
• 0
1
vote
4
replies
972
views
Subsampling when adjusting the read start sites in the ATACseqQC guide
atacseqqc
r
3.8 years ago
Arpi Beshlikyan
• 0
1
vote
2
replies
1.4k
views
ATACseqQC function bamSplit returns error when input .bam is from mouse
ATACseqQC
4.8 years ago
beiting
▴ 30
0
votes
3
replies
1.1k
views
package for ATACseq data analysis
SequencingData
ATACSeq
ATACseqQC
updated 20 months ago by
Rory Stark
★ 5.2k • written 2.6 years ago by
adR
▴ 30
35 results • Page
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Comment: Limma without eBayes, is it indistunguishable from Ordinary Least Square?
by
nbay13
• 0
yes my mistake I mixed the equation up while copying into the reply box. Should have been: ```{r} 2 * (1 - pt(abs(tstat), df = df.residual…
Comment: Getting Error in hclust(d, method = method): NA/NaN/Inf in foreign function call
by
angelathuynh5
• 0
Thank you for your response. To clarify, the process of making a heatmap performs rowscaling so it takes the value - (mean/std). And to res…
Comment: Limma without eBayes, is it indistunguishable from Ordinary Least Square?
by
Gordon Smyth
50k
The formula given in the original question is correct and yours is not. Your formula isn't even constrained to be between 0 and 1. Here is …
Comment: Limma without eBayes, is it indistunguishable from Ordinary Least Square?
by
nbay13
• 0
EDIT: removed
Comment: Method to find pathways different between 2 groups
by
Gordon Smyth
50k
sigPathway is another method that does not account for inter-gene correlation and which gives inflated significance, as we showed in our 20…
Votes
Answer: Getting Error in hclust(d, method = method): NA/NaN/Inf in foreign function call
Answer: error in limma , contrast.matrix Number of rows of contrast matrix must match nu
Answer: Extremely small p-values using Limma for proteomic data
Answer: How to save the DEXSeq results
Answer: minfi support of illumina Infinium methylationEPIC v2.0
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