Showing : ATACseqQC • reset
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Error with BSgenome, wanting to analyse non-model species with ATACseqQC
ATACseqQC
updated 22 months ago by 68k • written 22 months ago by • 0
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0
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652
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Issue with shiftGAlignmentsList() in ATACseqQC after updating
R ATACseqQC
22 months ago danalvoronov ▴ 10
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7
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1.8k
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ATACseqQC shiftGAlignmentsList() problem
ATACseqQC ATACSeq
updated 22 months ago by ▴ 10 • written 2.1 years ago by • 0
0
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1
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1.1k
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Error in ATACseqQC bamQC analysis
ATACSeq ATACseqQC
updated 3.0 years ago by ★ 1.3k • written 3.0 years ago by • 0
0
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0
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1.0k
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[ATACseqQC] NA values in sigs makes heatmap not completed
ATACseqQC ATACSeq
3.8 years ago hyjforesight • 0
1
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7
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2.3k
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TSSEscore function in ATACseqQC package
ATACseqQC
4.0 years ago • updated 3.9 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 3.4 years ago by ★ 5.2k • written 4.3 years ago by ▴ 40
0
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0
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752
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ATACseqQC function fragSizeDist returns error
fragSizeDist ATACseqQC
4.4 years ago xuyao15927402897 • 0
0
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0
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853
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NAs in TSSE for certain windows
ATACseqQC
4.4 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
4.6 years ago Nolan • 0
0
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9
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5.8k
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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
4.7 years ago Xiaojie Cheng • 0
1
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4
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1.8k
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How to use a fimo BED output as GRanges object in factorFootprints from ATACseqQC
ATACseqQC
updated 5.4 years ago by ★ 4.3k • written 5.4 years ago by ▴ 10
0
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4
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3.1k
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ATACseqQC R package for QC scores (TSS, FRIP, NFR, IDR)
ATACseqQC atacseq R
updated 5.4 years ago by ★ 1.3k • written 5.4 years ago by • 0
1
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2
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14k
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Interpreting TSS Enrichment Score Summary
atacseq atacseqqc tss enrichment
updated 5.4 years ago by ★ 1.3k • written 5.4 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
5.4 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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2.5k
views
ATACseqQC installation fails at shiny step
ATACseqQC
updated 6.4 years ago by 68k • written 6.4 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 6.4 years ago by ★ 4.3k • written 6.4 years ago by • 0
1
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2
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2.0k
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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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3.6k
views
ATAC-QC shiftGAlignmentsList function
ATAC-seq ATACseqQC
updated 6.5 years ago by ★ 4.3k • written 6.5 years ago by • 0
0
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7
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2.4k
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ATACseqQC splitGAlignmentsByCut: strand values must be in '+' '-' '*'
ATACseqQC R
updated 6.5 years ago by ★ 4.3k • written 6.5 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 6.5 years ago by ★ 4.3k • written 6.5 years ago by • 0
0
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7
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2.6k
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ATACseqQC shiftGAlignmentsList leads to (all(elementNROWS)>3) is not TRUE error
ATACseqQC ATAC ATACseq software error Tutorial
updated 6.6 years ago by ★ 13k • written 6.6 years ago by • 0
0
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6
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2.8k
views
atacseqQC error while splittin the bamfile
ATACseqQC ATAC-seq error split bam file
updated 6.7 years ago by • 0 • written 6.7 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
6.8 years ago Gary ▴ 20
2
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5
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2.1k
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The meaning of results produced by the bamQC function implemented in the ATACseqQC
ATACseqQC bamQC ATAC-Seq totalQNAMEs MAPQ
updated 6.9 years ago by ★ 4.3k • written 6.9 years ago by ▴ 20
11
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21
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7.3k
views
How about our ATAC-Seq data quality analyzed by ATACseqQC
ATACseqQC ATAC-Seq quality analysis fragment size distribution library complexity
updated 6.9 years ago by ★ 4.3k • written 6.9 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 7.5 years ago by ★ 1.3k • written 7.5 years ago by ▴ 10
0
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9
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2.3k
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use factorFootprints function in ATACseqQC to get DNA footprinting for certain gene region
ATACseqQC
updated 7.5 years ago by ★ 4.3k • written 7.5 years ago by ▴ 10
0
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1
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1.5k
views
ATACseqQC: a few questions
ATACseqQC
updated 7.5 years ago by ★ 4.3k • written 7.5 years ago by • 0
0
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1
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1.3k
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ATACseqQC questions in R language
atacseqqc
updated 7.6 years ago by ★ 1.3k • written 7.6 years ago by • 0
0
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1
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2.3k
views
Issue installing packages ATACseqQC and GO.db
GO.db biocinstaller package installation atacseqqc
updated 7.8 years ago by ★ 1.3k • written 7.8 years ago by • 0
0
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7
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3.1k
views
ATACseqQC memory overflow issue
atac-seq software error atacseqqc
updated 7.9 years ago by • 0 • written 7.9 years ago by ▴ 10
0
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2
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1.5k
views
ATACseqQC needs too much memory
ATACseqQC
updated 8.1 years ago by ★ 4.3k • written 8.1 years ago by • 0
5
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9
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5.3k
views
mm10 phastCons data for use with ATACseqQC
ATACseqQC bsgenome phastcons rtracklayer
updated 8.6 years ago by ★ 1.3k • written 8.6 years ago by ▴ 10
35 results • Page 1 of 1
Recent ...
Replies
Comment: Joining different datasets and analyzing using the group-specific condition effe by James W. MacDonald 68k
There is an example of how you can do this in the [DESeq vignette][1]. An alternative would be to fit a linear mixed model using the `vari…
Comment: Joining different datasets and analyzing using the group-specific condition effe by jason.chai • 0
@mikelove Could I please ask if a similar method would work my set of samples? I have 255 samples which have been generated from 76 subject…
Comment: Clarification on counting in Rsubread (featureCounts) by Luca • 0
Thanks to both of you for your helpful suggestions. The counting was already strand-specific at both the exon and gene levels. I resolved …
Comment: Clarification on counting in Rsubread (featureCounts) by Gordon Smyth 53k
Have you told featureCounts to do strand-specific counting? As pointed out by Frances Turner, you can lose reads if they overlap the gene …
Answer: Clarification on counting in Rsubread (featureCounts) by Frances Turner ▴ 20
You should look at the summary files produced by feature counts. This gives a breakdown of what happened to reads that were not assigned. Y…
Votes
A: DESeq2: What is the unit of DESeq2 normalized read count (VST)? Is it tag per mi
Answer: Clarification on counting in Rsubread (featureCounts)
Comment: Clarification on counting in Rsubread (featureCounts)
C: ControlGenes/ housekeeping genes Deseq2
Answer: Clarification on counting in Rsubread (featureCounts)
Awards • All
Commentator to James W. MacDonald 68k
Great Question to fl ▴ 20
Popular Question to Lluís Revilla Sancho ▴ 760
Popular Question to Gordon Smyth 53k
Popular Question to Aleena_Ensembl ▴ 30
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