Showing : ATACSeqQC • reset
1
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614
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Error with BSgenome, wanting to analyse non-model species with ATACseqQC
ATACseqQC
updated 21 months ago by 68k • written 21 months ago by • 0
0
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0
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625
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Issue with shiftGAlignmentsList() in ATACseqQC after updating
R ATACseqQC
21 months ago danalvoronov ▴ 10
0
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7
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1.7k
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ATACseqQC shiftGAlignmentsList() problem
ATACseqQC ATACSeq
updated 21 months ago by ▴ 10 • written 2.0 years ago by • 0
0
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1
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1.0k
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Error in ATACseqQC bamQC analysis
ATACSeq ATACseqQC
updated 2.9 years ago by ★ 1.3k • written 2.9 years ago by • 0
0
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0
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981
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[ATACseqQC] NA values in sigs makes heatmap not completed
ATACseqQC ATACSeq
3.7 years ago hyjforesight • 0
1
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7
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2.2k
views
TSSEscore function in ATACseqQC package
ATACseqQC
3.9 years ago • updated 3.8 years ago Liu Yu-Yu • 0
0
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3
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1.8k
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package for ATACseq data analysis
SequencingData ATACSeq ATACseqQC
updated 3.3 years ago by ★ 5.2k • written 4.2 years ago by ▴ 40
0
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0
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730
views
ATACseqQC function fragSizeDist returns error
fragSizeDist ATACseqQC
4.3 years ago xuyao15927402897 • 0
0
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0
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820
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NAs in TSSE for certain windows
ATACseqQC
4.3 years ago red_bricks ▴ 60
0
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2
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2.3k
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*** caught segfault *** address 0xffffffff9a378e20, cause 'memory not mapped'
ATACseqQC
4.5 years ago Nolan • 0
0
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9
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5.6k
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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
4.6 years ago Xiaojie Cheng • 0
1
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4
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1.7k
views
How to use a fimo BED output as GRanges object in factorFootprints from ATACseqQC
ATACseqQC
updated 5.3 years ago by ★ 4.3k • written 5.3 years ago by ▴ 10
0
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4
replies
3.0k
views
ATACseqQC R package for QC scores (TSS, FRIP, NFR, IDR)
ATACseqQC atacseq R
updated 5.3 years ago by ★ 1.3k • written 5.3 years ago by • 0
1
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2
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14k
views
Interpreting TSS Enrichment Score Summary
atacseq atacseqqc tss enrichment
updated 5.3 years ago by ★ 1.3k • written 5.3 years ago by • 0
1
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4
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1.5k
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Subsampling when adjusting the read start sites in the ATACseqQC guide
atacseqqc r
5.3 years ago Arpi Beshlikyan • 0
0
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5
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2.2k
views
ATACSeqQC - error when splitting files using mm10
atacseqqc atac-seq R bioconductor rsamtools
updated 5.5 years ago by ★ 4.0k • written 5.5 years ago by • 0
0
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5
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2.5k
views
ATACseqQC installation fails at shiny step
ATACseqQC
updated 6.2 years ago by 68k • written 6.2 years ago by • 0
0
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2
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1.4k
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factorFootprints, bindingSites and Profile.segmentation
ATACSeqQC factorFootprints
updated 6.3 years ago by ★ 4.3k • written 6.3 years ago by • 0
1
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2
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1.9k
views
ATACseqQC function bamSplit returns error when input .bam is from mouse
ATACseqQC
6.3 years ago beiting ▴ 30
1
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11
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3.4k
views
ATAC-QC shiftGAlignmentsList function
ATAC-seq ATACseqQC
updated 6.4 years ago by ★ 4.3k • written 6.4 years ago by • 0
0
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7
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2.3k
views
ATACseqQC splitGAlignmentsByCut: strand values must be in '+' '-' '*'
ATACseqQC R
updated 6.4 years ago by ★ 4.3k • written 6.4 years ago by • 0
0
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1
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1.5k
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ATAC-QC fragSizeDist function
ATAC-seq ATACseqQC
updated 6.4 years ago by ★ 4.3k • written 6.4 years ago by • 0
0
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7
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2.6k
views
ATACseqQC shiftGAlignmentsList leads to (all(elementNROWS)>3) is not TRUE error
ATACseqQC ATAC ATACseq software error Tutorial
updated 6.5 years ago by ★ 13k • written 6.5 years ago by • 0
0
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6
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2.7k
views
atacseqQC error while splittin the bamfile
ATACseqQC ATAC-seq error split bam file
updated 6.6 years ago by • 0 • written 6.6 years ago by ▴ 10
0
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0
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1.2k
views
Enough cell number or not based on library complexity evaluation by ATACseqQC?
ATACseqQC ATAC-Seq Library complexity estimateLibComplexity
6.7 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 6.8 years ago by ★ 4.3k • written 6.8 years ago by ▴ 20
11
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21
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7.1k
views
How about our ATAC-Seq data quality analyzed by ATACseqQC
ATACseqQC ATAC-Seq quality analysis fragment size distribution library complexity
updated 6.8 years ago by ★ 4.3k • written 6.8 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 7.4 years ago by ★ 1.3k • written 7.4 years ago by ▴ 10
0
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9
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2.3k
views
use factorFootprints function in ATACseqQC to get DNA footprinting for certain gene region
ATACseqQC
updated 7.4 years ago by ★ 4.3k • written 7.4 years ago by ▴ 10
0
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1
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1.4k
views
ATACseqQC: a few questions
ATACseqQC
updated 7.4 years ago by ★ 4.3k • written 7.4 years ago by • 0
0
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1
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1.3k
views
ATACseqQC questions in R language
atacseqqc
updated 7.5 years ago by ★ 1.3k • written 7.5 years ago by • 0
0
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1
reply
2.2k
views
Issue installing packages ATACseqQC and GO.db
GO.db biocinstaller package installation atacseqqc
updated 7.7 years ago by ★ 1.3k • written 7.7 years ago by • 0
0
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7
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3.0k
views
ATACseqQC memory overflow issue
atac-seq software error atacseqqc
updated 7.8 years ago by • 0 • written 7.8 years ago by ▴ 10
0
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2
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1.5k
views
ATACseqQC needs too much memory
ATACseqQC
updated 8.0 years ago by ★ 4.3k • written 8.0 years ago by • 0
5
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9
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5.1k
views
mm10 phastCons data for use with ATACseqQC
ATACseqQC bsgenome phastcons rtracklayer
updated 8.5 years ago by ★ 1.3k • written 8.5 years ago by ▴ 10
35 results • Page 1 of 1
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Answer: problem reading bam files into nucleR by James W. MacDonald 68k
The first step is to update to the current versions of R/Bioconductor and try again. It's possible that you have run into a bug that's alre…
Answer: Question about DESeq2 Design for Paired Treatment Study by ATpoint ★ 5.0k
It's a paired analysis so you don't need any patient-specific covariates such as age and sex. What you call batch effect might just be the …
Comment: problem reading bam files into nucleR by efoss ▴ 10
I thought I might be able to track down a problematic line in the bam file by repeatedly splitting the bam file in and then running the co…
Answer: two questions about limma by Gordon Smyth 53k
Answered here: https://support.bioconductor.org/p/16318/
Comment: Highly similar RNA-seq samples in PCA - pooling or technical duplication? by Ahmed Salah • 0
Thank you very much! will take that into consideration
Votes
Comment: Highly similar RNA-seq samples in PCA - pooling or technical duplication?
Answer: Large logFC but somewhat high FDR
Comment: upstream git branches of bioc-release
Comment: upstream git branches of bioc-release
Comment: upstream git branches of bioc-release
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