Showing : CHIPQC • reset
4
votes
13
replies
4.9k
views
BiocParallel error with ChIPQC
BiocManager ChIPQC RSamtools BiocParallel
updated 2.2 years ago by ★ 5.2k • written 2.8 years ago by • 0
3
votes
12
replies
4.4k
views
ChIPQC failling when run ChIPQC() over 6 samples
chipqc
updated 7.6 years ago by ▴ 420 • written 10.0 years ago by • 0
5
votes
11
replies
2.6k
views
ChIPQC Error in .Call2 NCList object is too deep
ChIPQC
updated 7.4 years ago by ▴ 420 • written 7.4 years ago by ▴ 10
3
votes
9
replies
3.6k
views
ChIPQC and broadPeak input
chipseq chipqc chip-seq
9.5 years ago lindahove ▴ 10
4
votes
8
replies
2.8k
views
ChIPQC v1.4 fails uninformatively where version 1.2 works fine
chipqc
updated 9.7 years ago by ★ 5.2k • written 9.9 years ago by ▴ 140
4
votes
8
replies
2.6k
views
ChIPQC and/or Diffbind - retrieving normalized read counts for peaks from single sample
DiffBind ChIPQC
9.1 years ago JD ▴ 10
1
vote
7
replies
3.4k
views
ChipQC not loading files
ChipQC diffbind
updated 6.6 years ago by ▴ 420 • written 6.6 years ago by • 0
0
votes
7
replies
2.5k
views
CHIPQC error regarding BiocParallel
CHIPQC Diffbind chipseq rory stark Thomas Carroll
updated 2.6 years ago by ▴ 40 • written 4.9 years ago by ▴ 10
3
votes
7
replies
2.9k
views
ChIPQC for a single sample (disabling facets)
ChipQc chipqc
8.7 years ago Coby Viner ▴ 50
2
votes
7
replies
2.5k
views
How to generate custom annotation for rat genome rn6 in ChIPQC
ChIPQC annotation rn6
updated 15 months ago by • 0 • written 4.5 years ago by • 0
0
votes
6
replies
1.9k
views
ChiPQC: 1Error in 1:(2 * readlength(object)) : NA/NaN argument
ChiPQC
updated 6.1 years ago by 25k • written 6.1 years ago by • 0
3
votes
6
replies
1.7k
views
ChIPQCreport yields a cryptic error if "Replicate" data is not specified
ChIPQC chipqc
updated 8.5 years ago by ★ 5.2k • written 8.5 years ago by ▴ 50
4
votes
6
replies
2.4k
views
ChIPQC GRCh38 usage yields "Unsupported annotation:hg38"
chipqc ChIPQC
updated 8.5 years ago by ▴ 420 • written 8.5 years ago by ▴ 50
3
votes
6
replies
2.2k
views
Integer overflow issue with ChIPQC
ChIPQC Rstudio
updated 5.7 years ago by 25k • written 5.7 years ago by ▴ 30
3
votes
6
replies
16k
views
Error: Faceting variables must have at least one value when plotting with ChIPQC
ChipQC chipqc
updated 2.5 years ago by • 0 • written 8.6 years ago by ▴ 10
2
votes
6
replies
2.7k
views
ChIPQC: error during annotation compilation
ChIPQC
updated 6.5 years ago by ▴ 420 • written 6.5 years ago by ▴ 10
2
votes
5
replies
2.2k
views
Diffbind: dba.plot retrieve variance explained
diffbind chipqc
updated 7.5 years ago by ★ 5.2k • written 7.6 years ago by ▴ 60
2
votes
5
replies
2.5k
views
ChIPQC gives Error subscript contains out-of-bounds ranges with custom transcript database
chipqc
updated 7.8 years ago by ▴ 420 • written 7.8 years ago by • 0
3
votes
5
replies
3.0k
views
ChIPQC - can't read in bam files
chipqc chipqcreport
6.5 years ago molly_the_minotaur ▴ 30
2
votes
5
replies
1.9k
views
Error involving ChIPQCreport
ChIPQC
updated 8.0 years ago by ▴ 420 • written 8.0 years ago by • 0
0
votes
4
replies
2.2k
views
ATAC-Seq peaks quality control with ChIPQC package, but getting error
ATAC-Seq ChIPQC
updated 6.1 years ago by 68k • written 6.1 years ago by ▴ 10
2
votes
4
replies
3.6k
views
ChIPQC error: "names' attribute [9] must be the same length as the vector [7]"
ChIPQC
updated 3.6 years ago by • 0 • written 5.8 years ago by ▴ 20
3
votes
4
replies
1.7k
views
ChIPQC on samples without peaks and wrong total reads
chipqc
updated 8.5 years ago by ▴ 420 • written 8.5 years ago by ▴ 10
1
vote
4
replies
2.5k
views
ChIPQC: reads counts in bam do not match ones from samtools flagstat
chipqc
updated 10.0 years ago by ▴ 420 • written 10.0 years ago by • 0
0
votes
4
replies
2.1k
views
ChiPQC and paired-end data
ChIPQC ChIPQC
updated 10.7 years ago by ▴ 20 • written 10.7 years ago by ▴ 340
0
votes
4
replies
1.9k
views
Unhelpful Errors Running ChIPQC on Computing Cluster
chipqc chipqcreport
7.6 years ago • updated 7.5 years ago jared.andrews07 ▴ 30
0
votes
4
replies
1.6k
views
ChIPQC plotCoverageHist() and plotCC() not showing inputs
ChIPQC plotCoverageHist plotCC input
8.2 years ago atisou • 0
0
votes
4
replies
2.0k
views
ChIPQCreport Total number of duplicates differs from multiqc/fastqc & RelCC is Inf
ChIPQC ChIPQCreport
updated 7.8 years ago by ▴ 420 • written 7.8 years ago by ▴ 60
0
votes
4
replies
2.6k
views
ChIPQC error: "non-zero exit status"
software error package installation chipqc txdb.hsapiens.ucsc.hg18.knowngene
updated 6.7 years ago by 25k • written 6.7 years ago by • 0
1
vote
4
replies
1.8k
views
ChIPQC error: Error in generating sample data
ChIPQC
updated 8.9 years ago by ★ 5.2k • written 8.9 years ago by ▴ 30
0
votes
3
replies
1.2k
views
ChIPQC: Depths of coverage plot - Figure 1 of the ChIPQC report
ChIPQC
written 3.7 years ago by • 0
5
votes
3
replies
2.3k
views
ChIPQC error: "if (nrow(pv$binding) > 0) { : argument is of length zero"
chipqc
8.7 years ago Danielle Denisko ▴ 30
0
votes
3
replies
1.5k
views
Problems with double read counts on ChIPQC
chipqc
updated 8.5 years ago by • 0 • written 8.5 years ago by • 0
1
vote
3
replies
1.4k
views
ChIPQC installation does not force latest DiffBind version
chipqc diffbind chipqcreport
updated 7.8 years ago by ▴ 420 • written 7.8 years ago by ▴ 50
1
vote
3
replies
2.5k
views
ChipQC Error: first error: could not find function "seqlevels<-"
software error chipqc
7.7 years ago tirza.doniger ▴ 20
0
votes
3
replies
1.9k
views
ChIPQC failed on chrM
ChIPQC
updated 7.7 years ago by ▴ 420 • written 7.8 years ago by • 0
0
votes
3
replies
1.5k
views
ChIPQC reading more samples that it should
chipqc
7.7 years ago C T ▴ 140
1
vote
3
replies
1.4k
views
ChIPQC : ChIPQCreport(dba_object) getting error when drawing plotFribl
ChIPQC
7.7 years ago ZheFrench ▴ 60
0
votes
3
replies
1.6k
views
ChiPQC run time error
ChiPQC
updated 7.7 years ago by ▴ 420 • written 7.7 years ago by • 0
1
vote
3
replies
3.5k
views
Downsampling ChIP-seq BAM files with spike in normalization factor before feeding into Diffbind
diffbind chipseq chipqc
updated 4.4 years ago by ★ 5.2k • written 7.1 years ago by ▴ 10
0
votes
3
replies
1.5k
views
ChIPQC ERROR with "subscript out of bounds"
chipqc
6.2 years ago Chevy Xu • 0
2
votes
3
replies
2.2k
views
ChipQC 'names' attribute [9] must be the same length as the vector [2]'
chipqc
updated 10 months ago by • 0 • written 4.5 years ago by ▴ 60
0
votes
2
replies
3.8k
views
Problem loading bamfiles to ChIPQC
ChIPQC
10.2 years ago sergio.espeso-gil • 0
4
votes
2
replies
1.6k
views
ChIPQC : ChIPQCreport(experiment) swap memory overload
ChIPQC ChIPQCreport
updated 7.8 years ago by ▴ 420 • written 7.8 years ago by ▴ 60
1
vote
2
replies
1.3k
views
Could it be possible to get an older version of ChIPQC?
ChIPQC ChIP-seq DiffBind Rory_Stark
2.7 years ago • updated 2.6 years ago etiennedanis • 0
0
votes
2
replies
1.2k
views
ChIP-seq or CUT&RUN enrichment
ChIPQC ChIPpeakAnno
3.1 years ago Bogdan ▴ 670
0
votes
2
replies
1.2k
views
ChIPQC plots for input samples
chipqc
updated 7.7 years ago by ▴ 420 • written 7.7 years ago by ▴ 140
4
votes
2
replies
2.1k
views
Confusing error when running ChIPQC
chipqc chipseq
updated 9.5 years ago by ▴ 420 • written 9.5 years ago by ★ 7.9k
2
votes
2
replies
1.6k
views
ChIPQC gives Bam file has 297 contigs Error: subscript contains out-of-bounds indices
ChIP-seq ChIPQC QC
updated 5.6 years ago by ▴ 20 • written 6.1 years ago by ▴ 10
0
votes
2
replies
1.4k
views
ChIPQC error in previously working code (BAM association error)
chipqc
updated 2.3 years ago by • 0 • written 3.9 years ago by ▴ 50
50 results • Page 1 of 1
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Replies
Comment: DiffBind custom normalization factor by Abbie • 0
Hello! Thanks so much for adding dba.normalize and all the documentation in the manual! I'm hoping I can ask a follow-up question here. I…
Answer: CpGs with genomic positions greater than the chromosome size in EPICv2? by James W. MacDonald 68k
All of the annotation packages provided by Bioconductor are simply repackaging of existing data from one or more sources. In this case, the…
Comment: Using TPM from tximport of Salmon output for singscore by Kent • 0
Thank you for the suggestions Michael. Would you say that after filtering out the low count genes, `rlog(counts, blind = T)` is doing the s…
Comment: Using TPM from tximport of Salmon output for singscore by Michael Love 43k
For clustering generally we recommend `vst()` see the workflow for example. For working with individual samples, I can see how a scaling/t…
Comment: DESeq2 model - How to test case/control time course model when taking account wi by Michael Love 43k
I'd recommend working with a local statistician or someone familiar with linear models in R. I have to reserve my time on the support site …
Votes
clusterProfiler-GO enrichment Error
A: Machine learning in R book
Data preparation and Machine learning on time course RNAseq data
Data preparation and Machine learning on time course RNAseq data
Answer: Use of org.Rn.eg.db with GRCr8 reference genome
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