Showing : ATACseqQC • reset
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Error with BSgenome, wanting to analyse non-model species with ATACseqQC
ATACseqQC
updated 13 months ago by 68k • written 13 months ago by • 0
0
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0
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400
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Issue with shiftGAlignmentsList() in ATACseqQC after updating
R ATACseqQC
14 months ago danalvoronov ▴ 10
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7
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1.4k
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ATACseqQC shiftGAlignmentsList() problem
ATACseqQC ATACSeq
updated 13 months ago by ▴ 10 • written 17 months ago by • 0
0
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1
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861
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Error in ATACseqQC bamQC analysis
ATACSeq ATACseqQC
updated 2.3 years ago by ★ 1.3k • written 2.3 years ago by • 0
0
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0
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849
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[ATACseqQC] NA values in sigs makes heatmap not completed
ATACseqQC ATACSeq
3.1 years ago hyjforesight • 0
1
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7
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1.9k
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TSSEscore function in ATACseqQC package
ATACseqQC
3.2 years ago Liu Yu-Yu • 0
0
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3
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1.5k
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package for ATACseq data analysis
SequencingData ATACSeq ATACseqQC
updated 2.7 years ago by ★ 5.2k • written 3.5 years ago by ▴ 40
0
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0
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607
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ATACseqQC function fragSizeDist returns error
fragSizeDist ATACseqQC
3.7 years ago xuyao15927402897 • 0
0
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0
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695
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NAs in TSSE for certain windows
ATACseqQC
3.7 years ago red_bricks ▴ 60
0
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2
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2.0k
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*** caught segfault *** address 0xffffffff9a378e20, cause 'memory not mapped'
ATACseqQC
3.9 years ago Nolan • 0
0
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9
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5.0k
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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
4.0 years ago Xiaojie Cheng • 0
1
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4
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1.5k
views
How to use a fimo BED output as GRanges object in factorFootprints from ATACseqQC
ATACseqQC
updated 4.6 years ago by ★ 4.3k • written 4.7 years ago by ▴ 10
0
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4
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2.6k
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ATACseqQC R package for QC scores (TSS, FRIP, NFR, IDR)
ATACseqQC atacseq R
updated 4.7 years ago by ★ 1.3k • written 4.7 years ago by • 0
1
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2
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13k
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Interpreting TSS Enrichment Score Summary
atacseq atacseqqc tss enrichment
updated 4.7 years ago by ★ 1.3k • written 4.7 years ago by • 0
1
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4
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1.3k
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Subsampling when adjusting the read start sites in the ATACseqQC guide
atacseqqc r
4.7 years ago Arpi Beshlikyan • 0
0
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5
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1.9k
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ATACSeqQC - error when splitting files using mm10
atacseqqc atac-seq R bioconductor rsamtools
updated 4.9 years ago by ★ 4.0k • written 4.9 years ago by • 0
0
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5
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2.2k
views
ATACseqQC installation fails at shiny step
ATACseqQC
updated 5.6 years ago by 68k • written 5.6 years ago by • 0
0
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2
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1.2k
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factorFootprints, bindingSites and Profile.segmentation
ATACSeqQC factorFootprints
updated 5.7 years ago by ★ 4.3k • written 5.7 years ago by • 0
1
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2
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1.8k
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ATACseqQC function bamSplit returns error when input .bam is from mouse
ATACseqQC
5.7 years ago beiting ▴ 30
1
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11
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3.1k
views
ATAC-QC shiftGAlignmentsList function
ATAC-seq ATACseqQC
updated 5.8 years ago by ★ 4.3k • written 5.8 years ago by • 0
0
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7
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2.1k
views
ATACseqQC splitGAlignmentsByCut: strand values must be in '+' '-' '*'
ATACseqQC R
updated 5.8 years ago by ★ 4.3k • written 5.8 years ago by • 0
0
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1
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1.3k
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ATAC-QC fragSizeDist function
ATAC-seq ATACseqQC
updated 5.8 years ago by ★ 4.3k • written 5.8 years ago by • 0
0
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7
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2.2k
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ATACseqQC shiftGAlignmentsList leads to (all(elementNROWS)>3) is not TRUE error
ATACseqQC ATAC ATACseq software error Tutorial
updated 5.8 years ago by ★ 13k • written 5.8 years ago by • 0
0
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6
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2.4k
views
atacseqQC error while splittin the bamfile
ATACseqQC ATAC-seq error split bam file
updated 6.0 years ago by • 0 • written 6.0 years ago by ▴ 10
0
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0
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1.0k
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Enough cell number or not based on library complexity evaluation by ATACseqQC?
ATACseqQC ATAC-Seq Library complexity estimateLibComplexity
6.1 years ago Gary ▴ 20
2
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5
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1.8k
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The meaning of results produced by the bamQC function implemented in the ATACseqQC
ATACseqQC bamQC ATAC-Seq totalQNAMEs MAPQ
updated 6.2 years ago by ★ 4.3k • written 6.2 years ago by ▴ 20
11
votes
21
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6.4k
views
How about our ATAC-Seq data quality analyzed by ATACseqQC
ATACseqQC ATAC-Seq quality analysis fragment size distribution library complexity
updated 6.2 years ago by ★ 4.3k • written 6.2 years ago by ▴ 20
0
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3
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1.3k
views
Compare the DNA footprinting between different samples when using ATACseqQC
atacseqqc
updated 6.8 years ago by ★ 1.3k • written 6.8 years ago by ▴ 10
0
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9
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2.0k
views
use factorFootprints function in ATACseqQC to get DNA footprinting for certain gene region
ATACseqQC
updated 6.8 years ago by ★ 4.3k • written 6.8 years ago by ▴ 10
0
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1
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1.3k
views
ATACseqQC: a few questions
ATACseqQC
updated 6.8 years ago by ★ 4.3k • written 6.8 years ago by • 0
0
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1
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1.1k
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ATACseqQC questions in R language
atacseqqc
updated 6.9 years ago by ★ 1.3k • written 6.9 years ago by • 0
0
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1
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2.0k
views
Issue installing packages ATACseqQC and GO.db
GO.db biocinstaller package installation atacseqqc
updated 7.1 years ago by ★ 1.3k • written 7.1 years ago by • 0
0
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7
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2.7k
views
ATACseqQC memory overflow issue
atac-seq software error atacseqqc
updated 7.2 years ago by • 0 • written 7.2 years ago by ▴ 10
0
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2
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1.3k
views
ATACseqQC needs too much memory
ATACseqQC
updated 7.4 years ago by ★ 4.3k • written 7.4 years ago by • 0
5
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9
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4.7k
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mm10 phastCons data for use with ATACseqQC
ATACseqQC bsgenome phastcons rtracklayer
updated 7.9 years ago by ★ 1.3k • written 7.9 years ago by ▴ 10
35 results • Page 1 of 1
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Comment: Differing results with DESeq2 by JKim • 0
My two cents. I think it would be more straightforward if you use cellmeans model. Have a look at [A guide to creating design matrices for …
Answer: CluserProfiler message "No gene can be mapped" by James W. MacDonald 68k
Your gene IDs are things like this: `Mpyr-NLJ1B.v3.hap1.scaffold1.g290550`, and the genes in your term2gene table are things like this: `Mp…
Answer: RNA-seq input to GRaNIE by James W. MacDonald 68k
This is [covered in the vignette.][1] [1]: https://bioconductor.org/packages/release/bioc/vignettes/GRaNIE/inst/doc/GRaNIE_packageDe…
Answer: Help using reduceSimMatrix with a custom annotation by sergisayolspuig ▴ 80
Hi there, `reduceSimMatrix()` expects a "GOALL" keytype in the OrgDb object when called with `children=TRUE` (which is the default for thi…
Answer: Analyzing TnSeq data with DESeq2 by cold.wolverine.arku • 0
That's a great use case of DESeq2! Even though it's not specifically tailored for TnSeq data, your approach to normalize and run explorator…
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A: Unbalanced experiment with multiple samples from each patient.
A: Understanding contrasts limma
Answer: ROAST for small sets
Answer: ROAST for small sets
A: conceptual question about FDR, FDR adjusted p-value and q-value
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