Showing : ATACSeqQC • reset
1
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Error with BSgenome, wanting to analyse non-model species with ATACseqQC
ATACseqQC
updated 23 months ago by 68k • written 23 months ago by • 0
0
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0
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659
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Issue with shiftGAlignmentsList() in ATACseqQC after updating
R ATACseqQC
23 months ago danalvoronov ▴ 10
0
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7
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1.9k
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ATACseqQC shiftGAlignmentsList() problem
ATACseqQC ATACSeq
updated 23 months ago by ▴ 10 • written 2.2 years ago by • 0
0
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1
reply
1.1k
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Error in ATACseqQC bamQC analysis
ATACSeq ATACseqQC
updated 3.1 years ago by ★ 1.3k • written 3.1 years ago by • 0
0
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0
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1.1k
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[ATACseqQC] NA values in sigs makes heatmap not completed
ATACseqQC ATACSeq
3.9 years ago hyjforesight • 0
1
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7
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2.3k
views
TSSEscore function in ATACseqQC package
ATACseqQC
4.1 years ago • updated 4.0 years ago Liu Yu-Yu • 0
0
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3
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1.9k
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package for ATACseq data analysis
SequencingData ATACSeq ATACseqQC
updated 3.5 years ago by ★ 5.3k • written 4.4 years ago by ▴ 40
0
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0
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765
views
ATACseqQC function fragSizeDist returns error
fragSizeDist ATACseqQC
4.5 years ago xuyao15927402897 • 0
0
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0
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875
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NAs in TSSE for certain windows
ATACseqQC
4.5 years ago red_bricks ▴ 60
0
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2
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2.4k
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*** caught segfault *** address 0xffffffff9a378e20, cause 'memory not mapped'
ATACseqQC
4.7 years ago Nolan • 0
0
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9
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6.1k
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No peak corresponding to the nucleosome-free regions is observed in Fragment size distribution of ATAC-seq
ATACseqQC Fragmentsizedistribution ATAC-seq
4.8 years ago Xiaojie Cheng • 0
1
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4
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1.8k
views
How to use a fimo BED output as GRanges object in factorFootprints from ATACseqQC
ATACseqQC
updated 5.5 years ago by ★ 4.3k • written 5.5 years ago by ▴ 10
0
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4
replies
3.3k
views
ATACseqQC R package for QC scores (TSS, FRIP, NFR, IDR)
ATACseqQC atacseq R
updated 5.5 years ago by ★ 1.3k • written 5.5 years ago by • 0
1
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2
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15k
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Interpreting TSS Enrichment Score Summary
atacseq atacseqqc tss enrichment
updated 5.5 years ago by ★ 1.3k • written 5.5 years ago by • 0
1
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4
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1.5k
views
Subsampling when adjusting the read start sites in the ATACseqQC guide
atacseqqc r
5.5 years ago Arpi Beshlikyan • 0
0
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5
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2.3k
views
ATACSeqQC - error when splitting files using mm10
atacseqqc atac-seq R bioconductor rsamtools
updated 5.7 years ago by ★ 4.0k • written 5.7 years ago by • 0
0
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5
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2.6k
views
ATACseqQC installation fails at shiny step
ATACseqQC
updated 6.5 years ago by 68k • written 6.5 years ago by • 0
0
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2
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1.5k
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factorFootprints, bindingSites and Profile.segmentation
ATACSeqQC factorFootprints
updated 6.5 years ago by ★ 4.3k • written 6.5 years ago by • 0
1
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2
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2.0k
views
ATACseqQC function bamSplit returns error when input .bam is from mouse
ATACseqQC
6.5 years ago beiting ▴ 30
1
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11
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3.7k
views
ATAC-QC shiftGAlignmentsList function
ATAC-seq ATACseqQC
updated 6.6 years ago by ★ 4.3k • written 6.6 years ago by • 0
0
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7
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2.5k
views
ATACseqQC splitGAlignmentsByCut: strand values must be in '+' '-' '*'
ATACseqQC R
updated 6.6 years ago by ★ 4.3k • written 6.6 years ago by • 0
0
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1
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1.5k
views
ATAC-QC fragSizeDist function
ATAC-seq ATACseqQC
updated 6.6 years ago by ★ 4.3k • written 6.6 years ago by • 0
0
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7
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2.7k
views
ATACseqQC shiftGAlignmentsList leads to (all(elementNROWS)>3) is not TRUE error
ATACseqQC ATAC ATACseq software error Tutorial
updated 6.7 years ago by ★ 13k • written 6.7 years ago by • 0
0
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6
replies
2.8k
views
atacseqQC error while splittin the bamfile
ATACseqQC ATAC-seq error split bam file
updated 6.8 years ago by • 0 • written 6.8 years ago by ▴ 10
0
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0
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1.2k
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Enough cell number or not based on library complexity evaluation by ATACseqQC?
ATACseqQC ATAC-Seq Library complexity estimateLibComplexity
6.9 years ago Gary ▴ 20
2
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5
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2.1k
views
The meaning of results produced by the bamQC function implemented in the ATACseqQC
ATACseqQC bamQC ATAC-Seq totalQNAMEs MAPQ
updated 7.0 years ago by ★ 4.3k • written 7.0 years ago by ▴ 20
11
votes
21
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7.6k
views
How about our ATAC-Seq data quality analyzed by ATACseqQC
ATACseqQC ATAC-Seq quality analysis fragment size distribution library complexity
updated 7.0 years ago by ★ 4.3k • written 7.0 years ago by ▴ 20
0
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3
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1.5k
views
Compare the DNA footprinting between different samples when using ATACseqQC
atacseqqc
updated 7.6 years ago by ★ 1.3k • written 7.6 years ago by ▴ 10
0
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9
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2.4k
views
use factorFootprints function in ATACseqQC to get DNA footprinting for certain gene region
ATACseqQC
updated 7.6 years ago by ★ 4.3k • written 7.6 years ago by ▴ 10
0
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1
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1.5k
views
ATACseqQC: a few questions
ATACseqQC
updated 7.6 years ago by ★ 4.3k • written 7.6 years ago by • 0
0
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1
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1.3k
views
ATACseqQC questions in R language
atacseqqc
updated 7.7 years ago by ★ 1.3k • written 7.7 years ago by • 0
0
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1
reply
2.3k
views
Issue installing packages ATACseqQC and GO.db
GO.db biocinstaller package installation atacseqqc
updated 7.9 years ago by ★ 1.3k • written 7.9 years ago by • 0
0
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7
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3.2k
views
ATACseqQC memory overflow issue
atac-seq software error atacseqqc
updated 8.0 years ago by • 0 • written 8.0 years ago by ▴ 10
0
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2
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1.5k
views
ATACseqQC needs too much memory
ATACseqQC
updated 8.2 years ago by ★ 4.3k • written 8.2 years ago by • 0
5
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9
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5.4k
views
mm10 phastCons data for use with ATACseqQC
ATACseqQC bsgenome phastcons rtracklayer
updated 8.7 years ago by ★ 1.3k • written 8.7 years ago by ▴ 10
35 results • Page 1 of 1
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Comment: Which preprocessing steps are needed before running limpa? by miro165sabo • 0
Hi @gordonsmyth, thank you a lot for very fast and valuable response. I edited the question to provide more details.
Answer: Should I use beta1 from limpa::dpc() or limpa::dpcCN(), if they differ? by Gordon Smyth 53k
I tend to use dpcCN(), because it more robust than dpc() to experiments with lots of samples and big differences between samples. You coul…
Answer: Which preprocessing steps are needed before running limpa? by Gordon Smyth 53k
Please see the example limpa analyses given at <http://github.com/smythlab/limpa>, especially the kidney cancer case study. limpa does not…
Comment: Why does IDTaxa trainingSet for SILVA contain "_2" suffixes in the taxonomy name by Korneel • 0
Thanks for the quick reply! If I understand correctly, I think if I keep track of the full lineage, I shouldn't have any risk of collapsin…
Comment: Pathway abundance data from Curatedmetagenomics by yesquokkan • 0
Hello, I was also wondering about the same issue. Did you figure it out?
Votes
Answer: Which preprocessing steps are needed before running limpa?
Answer: Should I use beta1 from limpa::dpc() or limpa::dpcCN(), if they differ?
Answer: Which preprocessing steps are needed before running limpa?
Answer: Which preprocessing steps are needed before running limpa?
Answer: Should I use beta1 from limpa::dpc() or limpa::dpcCN(), if they differ?
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