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ATACseqQC
•
reset
0
votes
0
replies
61
views
[ATACseqQC] NA values in sigs makes heatmap not completed
ATACseqQC
ATACSeq
9 weeks ago
hyjforesight
• 0
1
vote
7
replies
437
views
TSSEscore function in ATACseqQC package
ATACseqQC
3 months ago
Liu Yu-Yu
• 0
0
votes
2
replies
241
views
package for ATACseq data analysis
SequencingData
ATACSeq
ATACseqQC
7 months ago
adR
▴ 10
0
votes
0
replies
128
views
ATACseqQC function fragSizeDist returns error
fragSizeDist
ATACseqQC
8 months ago
xuyao15927402897
• 0
0
votes
0
replies
130
views
NAs in TSSE for certain windows
ATACseqQC
8 months ago
red_bricks
▴ 50
0
votes
2
replies
507
views
*** caught segfault *** address 0xffffffff9a378e20, cause 'memory not mapped'
ATACseqQC
11 months ago
Nolan
• 0
0
votes
9
replies
917
views
No peak corresponding to the nucleosome-free regions is observed in Fragment size distribution of ATAC-seq
ATACseqQC
Fragmentsizedistribution
ATAC-seq
13 months ago • updated 12 months ago
Xiaojie Cheng
• 0
1
vote
4
replies
442
views
How to use a fimo BED output as GRanges object in factorFootprints from ATACseqQC
ATACseqQC
updated 20 months ago by
Julie Zhu
★ 4.3k • written 20 months ago by
pedro.rotcha
▴ 10
0
votes
4
replies
790
views
ATACseqQC R package for QC scores (TSS, FRIP, NFR, IDR)
ATACseqQC
atacseq
R
updated 21 months ago by
Ou, Jianhong
★ 1.3k • written 21 months ago by
achaillon
• 0
1
vote
2
replies
2.9k
views
Interpreting TSS Enrichment Score Summary
atacseq
atacseqqc
tss
enrichment
updated 21 months ago by
Ou, Jianhong
★ 1.3k • written 21 months ago by
Arpi Beshlikyan
• 0
1
vote
4
replies
383
views
Subsampling when adjusting the read start sites in the ATACseqQC guide
atacseqqc
r
21 months ago
Arpi Beshlikyan
• 0
0
votes
5
replies
561
views
ATACSeqQC - error when splitting files using mm10
atacseqqc
atac-seq
R
bioconductor
rsamtools
updated 2.0 years ago by
Kevin Blighe
3.5k • written 2.0 years ago by
rita.monteiro
• 0
0
votes
5
replies
792
views
ATACseqQC installation fails at shiny step
ATACseqQC
updated 2.7 years ago by
James W. MacDonald
59k • written 2.7 years ago by
kesarwani.anil
• 0
0
votes
2
replies
485
views
factorFootprints, bindingSites and Profile.segmentation
ATACSeqQC
factorFootprints
updated 2.8 years ago by
Julie Zhu
★ 4.3k • written 2.8 years ago by
Nick Gomez
• 0
1
vote
2
replies
680
views
ATACseqQC function bamSplit returns error when input .bam is from mouse
ATACseqQC
2.8 years ago
beiting
▴ 30
1
vote
11
replies
986
views
ATAC-QC shiftGAlignmentsList function
ATAC-seq
ATACseqQC
updated 2.8 years ago by
Julie Zhu
★ 4.3k • written 2.9 years ago by
Shuang He
• 0
0
votes
7
replies
622
views
ATACseqQC splitGAlignmentsByCut: strand values must be in '+' '-' '*'
ATACseqQC
R
updated 2.9 years ago by
Julie Zhu
★ 4.3k • written 2.9 years ago by
mbasam
• 0
0
votes
1
reply
417
views
ATAC-QC fragSizeDist function
ATAC-seq
ATACseqQC
updated 2.9 years ago by
Julie Zhu
★ 4.3k • written 2.9 years ago by
Shuang He
• 0
0
votes
7
replies
853
views
ATACseqQC shiftGAlignmentsList leads to (all(elementNROWS)>3) is not TRUE error
ATACseqQC
ATAC
ATACseq
software error
Tutorial
updated 2.9 years ago by
Steve Lianoglou
13k • written 2.9 years ago by
mbasam
• 0
0
votes
6
replies
1.1k
views
atacseqQC error while splittin the bamfile
ATACseqQC
ATAC-seq
error
split bam file
updated 3.0 years ago by
contact
• 0 • written 3.0 years ago by
theodore.georgomanolis
• 0
0
votes
0
replies
394
views
Enough cell number or not based on library complexity evaluation by ATACseqQC?
ATACseqQC
ATAC-Seq
Library complexity
estimateLibComplexity
3.2 years ago
Gary
▴ 20
2
votes
5
replies
732
views
The meaning of results produced by the bamQC function implemented in the ATACseqQC
ATACseqQC
bamQC
ATAC-Seq
totalQNAMEs
MAPQ
updated 3.2 years ago by
Julie Zhu
★ 4.3k • written 3.3 years ago by
Gary
▴ 20
11
votes
21
replies
2.9k
views
How about our ATAC-Seq data quality analyzed by ATACseqQC
ATACseqQC
ATAC-Seq
quality analysis
fragment size distribution
library complexity
updated 3.3 years ago by
Julie Zhu
★ 4.3k • written 3.3 years ago by
Gary
▴ 20
0
votes
3
replies
509
views
Compare the DNA footprinting between different samples when using ATACseqQC
atacseqqc
updated 3.8 years ago by
Ou, Jianhong
★ 1.3k • written 3.8 years ago by
aimin.at.work
▴ 10
0
votes
9
replies
713
views
use factorFootprints function in ATACseqQC to get DNA footprinting for certain gene region
ATACseqQC
updated 3.9 years ago by
Julie Zhu
★ 4.3k • written 3.9 years ago by
aimin.at.work
▴ 10
0
votes
1
reply
558
views
ATACseqQC: a few questions
ATACseqQC
updated 3.9 years ago by
Julie Zhu
★ 4.3k • written 3.9 years ago by
david.mckinnon
• 0
0
votes
1
reply
448
views
ATACseqQC questions in R language
atacseqqc
updated 4.0 years ago by
Ou, Jianhong
★ 1.3k • written 4.0 years ago by
rsong
• 0
0
votes
1
reply
979
views
Issue installing packages ATACseqQC and GO.db
GO.db
biocinstaller
package installation
atacseqqc
updated 4.2 years ago by
Ou, Jianhong
★ 1.3k • written 4.2 years ago by
n.pantelireis16
• 0
0
votes
7
replies
1.2k
views
ATACseqQC memory overflow issue
atac-seq
software error
atacseqqc
updated 4.2 years ago by
Haibo.Liu
• 0 • written 4.3 years ago by
José Luis Lavín
▴ 10
0
votes
2
replies
626
views
ATACseqQC needs too much memory
ATACseqQC
updated 4.5 years ago by
Julie Zhu
★ 4.3k • written 4.5 years ago by
mdurante14
• 0
5
votes
9
replies
2.3k
views
mm10 phastCons data for use with ATACseqQC
ATACseqQC
bsgenome
phastcons
rtracklayer
updated 5.0 years ago by
Ou, Jianhong
★ 1.3k • written 5.0 years ago by
crysis405
▴ 10
31 results • Page
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Replies
Comment: performing the differential binding in ChIP-seq
by
Bogdan
▴ 640
Thank you. Yes, DiffBind might be a good choice shall we have replicates per sample. Another choice is MA-norm2. Any other well-tested sug…
Comment: Error using read.ilmn and neqc
by
Gordon Smyth
45k
I edited the title of your question to be more specific.
Answer: Using limma to read Illumina HT-12 v4 data
by
Gordon Smyth
45k
It seems clear that you haven't exported the correct intensity data from GenomeStudio, and I think you recognize that yourself in your ques…
Answer: performing the differential binding in ChIP-seq
by
etiennedanis
• 0
DiffBind https://bioconductor.org/packages/release/bioc/html/DiffBind.html
Comment: Transcript-level differential expression using DESeq2
by
Michael Love
36k
Did you see the part of the vignette where we talk about this? https://bioconductor.org/packages/release/bioc/vignettes/fishpond/inst/doc/…
Votes
Comment: Using vegan::betadisper for determing if I subset my design for DESeq2
Answer: How to best visualize multi-level transcriptomics experiment data?
A: Interpreting results of sample-to-sample PCA/clustering and changing assignment
C: DESeq2 - Differences between plotCounts and normalized counts
C: DESEq2 - Change reference level change "Contrasts" results
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