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atacseqqc
•
reset
1
Vote
4
Replies
117
Views
How to use a fimo BED output as GRanges object in factorFootprints from ATACseqQC
ATACseqQC
4 months ago
pedro.rotcha
• 10
• updated 4 months ago
Julie Zhu
♦ 4.2k
0
Votes
4
Replies
161
Views
ATACseqQC R package for QC scores (TSS, FRIP, NFR, IDR)
ATACseqQC
atacseq
R
4 months ago
achaillon
• 0
• updated 4 months ago
Ou, Jianhong
♦ 1.2k
1
Vote
2
Replies
496
Views
Interpreting TSS Enrichment Score Summary
atacseq
atacseqqc
tss
enrichment
5 months ago
Arpi Beshlikyan
• 0
• updated 5 months ago
Ou, Jianhong
♦ 1.2k
1
Vote
4
Replies
90
Views
Subsampling when adjusting the read start sites in the ATACseqQC guide
atacseqqc
r
5 months ago
Arpi Beshlikyan
• 0
0
Votes
5
Replies
140
Views
ATACSeqQC - error when splitting files using mm10
atacseqqc
atac-seq
R
bioconductor
rsamtools
8 months ago
rita.monteiro
• 0
• updated 8 months ago
Kevin Blighe
2.3k
0
Votes
5
Replies
249
Views
ATACseqQC installation fails at shiny step
ATACseqQC
16 months ago
kesarwani.anil
• 0
• updated 16 months ago
James W. MacDonald
55k
0
Votes
2
Replies
230
Views
factorFootprints, bindingSites and Profile.segmentation
ATACSeqQC
factorFootprints
17 months ago
Nick Gomez
• 0
• updated 17 months ago
Julie Zhu
♦ 4.2k
1
Vote
2
Replies
304
Views
ATACseqQC function bamSplit returns error when input .bam is from mouse
ATACseqQC
17 months ago
beiting
• 30
1
Vote
11
Replies
462
Views
ATAC-QC shiftGAlignmentsList function
ATAC-seq
ATACseqQC
18 months ago
Shuang He
• 0
• updated 18 months ago
Julie Zhu
♦ 4.2k
0
Votes
7
Replies
294
Views
ATACseqQC splitGAlignmentsByCut: strand values must be in '+' '-' '*'
ATACseqQC
R
18 months ago
mbasam
• 0
• updated 18 months ago
Julie Zhu
♦ 4.2k
0
Votes
1
Reply
168
Views
ATAC-QC fragSizeDist function
ATAC-seq
ATACseqQC
18 months ago
Shuang He
• 0
• updated 18 months ago
Julie Zhu
♦ 4.2k
0
Votes
7
Replies
369
Views
ATACseqQC shiftGAlignmentsList leads to (all(elementNROWS)>3) is not TRUE error
ATACseqQC
ATAC
ATACseq
software error
Tutorial
19 months ago
mbasam
• 0
• updated 19 months ago
Steve Lianoglou
13k
0
Votes
6
Replies
560
Views
atacseqQC error while splittin the bamfile
ATACseqQC
ATAC-seq
error
split bam file
20 months ago
theodore.georgomanolis
• 0
• updated 20 months ago
contact
• 0
0
Votes
0
Replies
233
Views
Enough cell number or not based on library complexity evaluation by ATACseqQC?
ATACseqQC
ATAC-Seq
Library complexity
estimateLibComplexity
22 months ago
Gary
• 20
2
Votes
5
Replies
364
Views
The meaning of results produced by the bamQC function implemented in the ATACseqQC
ATACseqQC
bamQC
ATAC-Seq
totalQNAMEs
MAPQ
23 months ago
Gary
• 20
• updated 23 months ago
Julie Zhu
♦ 4.2k
11
Votes
21
Replies
1.8k
Views
How about our ATAC-Seq data quality analyzed by ATACseqQC
ATACseqQC
ATAC-Seq
quality analysis
fragment size distribution
library complexity
23 months ago
Gary
• 20
• updated 23 months ago
Julie Zhu
♦ 4.2k
0
Votes
3
Replies
313
Views
Compare the DNA footprinting between different samples when using ATACseqQC
atacseqqc
2.5 years ago
aimin.at.work
• 10
• updated 2.5 years ago
Ou, Jianhong
♦ 1.2k
0
Votes
9
Replies
394
Views
use factorFootprints function in ATACseqQC to get DNA footprinting for certain gene region
ATACseqQC
2.5 years ago
aimin.at.work
• 10
• updated 2.5 years ago
Julie Zhu
♦ 4.2k
0
Votes
1
Reply
360
Views
ATACseqQC: a few questions
ATACseqQC
2.5 years ago
david.mckinnon
• 0
• updated 2.5 years ago
Julie Zhu
♦ 4.2k
0
Votes
1
Reply
270
Views
ATACseqQC questions in R language
atacseqqc
2.6 years ago
rsong
• 0
• updated 2.6 years ago
Ou, Jianhong
♦ 1.2k
0
Votes
1
Reply
680
Views
Issue installing packages ATACseqQC and GO.db
GO.db
biocinstaller
package installation
atacseqqc
2.8 years ago
n.pantelireis16
• 0
• updated 2.8 years ago
Ou, Jianhong
♦ 1.2k
0
Votes
7
Replies
754
Views
ATACseqQC memory overflow issue
atac-seq
software error
atacseqqc
2.9 years ago
José Luis Lavín
• 10
• updated 2.9 years ago
Haibo.Liu
• 0
0
Votes
2
Replies
446
Views
ATACseqQC needs too much memory
ATACseqQC
3.1 years ago
mdurante14
• 0
• updated 3.1 years ago
Julie Zhu
♦ 4.2k
5
Votes
9
Replies
1.7k
Views
mm10 phastCons data for use with ATACseqQC
ATACseqQC
bsgenome
phastcons
rtracklayer
3.7 years ago
crysis405
• 10
• updated 3.7 years ago
Ou, Jianhong
♦ 1.2k
24 results • Page
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Comment: DESeq2 Error: ncol(countData) == nrow(colData) is not TRUE
by
Pedram
• 0
Hello Michael I could not make the same matrix although I did what you said
Comment: Replace a specific nucleotide sequence, at a specific position, with another in
by
Konstantinos Yeles
• 40
Hello @Benjamin-24571 for your example, I can suggest you this code: Read <- c("1","2","3","4") Sequences <- c("ACACCCACG", "AA…
Comment: CHIP Seq Analysis by DiffBind Package
by
shrinka.genetics
• 0
Hello Thanks for your reply. I changed my file format and now it ran. It gave one plot also. All file s are in same directory. No…
Answer: Installing Bioconductor packages in Docker
by
Konstantinos Yeles
• 40
Hello, @adklts-21974 My way to do the installation of packages in a docker is like this: FROM bioconductor/bioconductor_docker…
Comment: HTqPCR: dealing with technical replicates (filterCategory) and inability to anal
by
larissa.stanberry
• 0
I ran into the same issue. It appears that filtering does not carry over featureData with the exception of featureNames, e.g. call featureD…
Votes
A: single-cells RNA-seq analysis by MAST with unbalanced group size
single-cells RNA-seq analysis by MAST with unbalanced group size
A: single-cells RNA-seq analysis by MAST with unbalanced group size
A: DESeq2 1.20.0 lfcshrink function
DEXSeq Usage and Expression Confusion
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