Showing : ChipQc • reset
3
votes
12
replies
3.8k
views
ChIPQC failling when run ChIPQC() over 6 samples
chipqc
updated 6.7 years ago by ▴ 420 • written 9.1 years ago by • 0
3
votes
9
replies
2.9k
views
ChIPQC and broadPeak input
chipseq chipqc chip-seq
8.6 years ago lindahove ▴ 10
5
votes
11
replies
2.0k
views
ChIPQC Error in .Call2 NCList object is too deep
ChIPQC
updated 6.4 years ago by ▴ 420 • written 6.5 years ago by ▴ 10
4
votes
8
replies
2.3k
views
ChIPQC v1.4 fails uninformatively where version 1.2 works fine
chipqc
updated 8.8 years ago by ★ 5.1k • written 9.0 years ago by ▴ 140
0
votes
4
replies
1.6k
views
Unhelpful Errors Running ChIPQC on Computing Cluster
chipqc chipqcreport
6.7 years ago • updated 6.6 years ago jared.andrews07 ▴ 30
3
votes
6
replies
14k
views
Error: Faceting variables must have at least one value when plotting with ChIPQC
ChipQC chipqc
updated 18 months ago by • 0 • written 7.6 years ago by ▴ 10
0
votes
3
replies
1.3k
views
Problems with double read counts on ChIPQC
chipqc
updated 7.6 years ago by • 0 • written 7.6 years ago by • 0
2
votes
5
replies
1.5k
views
Error involving ChIPQCreport
ChIPQC
updated 7.0 years ago by ▴ 420 • written 7.1 years ago by • 0
4
votes
8
replies
2.2k
views
ChIPQC and/or Diffbind - retrieving normalized read counts for peaks from single sample
DiffBind ChIPQC
8.2 years ago JD ▴ 10
0
votes
3
replies
1.2k
views
ChIPQC reading more samples that it should
chipqc
6.8 years ago C T ▴ 140
3
votes
4
replies
1.4k
views
ChIPQC on samples without peaks and wrong total reads
chipqc
updated 7.6 years ago by ▴ 420 • written 7.6 years ago by ▴ 10
1
vote
3
replies
1.1k
views
ChIPQC installation does not force latest DiffBind version
chipqc diffbind chipqcreport
updated 6.8 years ago by ▴ 420 • written 6.8 years ago by ▴ 50
4
votes
2
replies
1.3k
views
ChIPQC : ChIPQCreport(experiment) swap memory overload
ChIPQC ChIPQCreport
updated 6.9 years ago by ▴ 420 • written 6.9 years ago by ▴ 40
0
votes
4
replies
1.8k
views
ChiPQC and paired-end data
ChIPQC ChIPQC
updated 9.7 years ago by ▴ 20 • written 9.8 years ago by ▴ 340
2
votes
5
replies
1.8k
views
Diffbind: dba.plot retrieve variance explained
diffbind chipqc
updated 6.6 years ago by ★ 5.1k • written 6.6 years ago by ▴ 40
1
vote
3
replies
2.7k
views
Downsampling ChIP-seq BAM files with spike in normalization factor before feeding into Diffbind
diffbind chipseq chipqc
updated 3.4 years ago by ★ 5.1k • written 6.1 years ago by ▴ 10
2
votes
6
replies
2.2k
views
ChIPQC: error during annotation compilation
ChIPQC
updated 5.6 years ago by ▴ 420 • written 5.6 years ago by ▴ 10
2
votes
1
reply
1.6k
views
DiffBind: Error in if (res$config$bCorPlot) { : the condition has length > 1
DiffBind ChIPQC
updated 19 months ago by ★ 5.1k • written 19 months ago by • 0
0
votes
1
reply
847
views
ChIPQC error: NCList object is too deep
ChIPQC
updated 5.2 years ago by ▴ 420 • written 5.3 years ago by • 0
0
votes
2
replies
3.2k
views
Problem loading bamfiles to ChIPQC
ChIPQC
9.2 years ago sergio.espeso-gil • 0
1
vote
4
replies
2.1k
views
ChIPQC: reads counts in bam do not match ones from samtools flagstat
chipqc
updated 9.1 years ago by ▴ 420 • written 9.1 years ago by • 0
3
votes
1
reply
3.2k
views
creating custom genome annotation for the ChIPQC package
ChIPSeq QC ChIPQC
updated 8.7 years ago by ▴ 420 • written 8.7 years ago by ▴ 160
4
votes
2
replies
1.7k
views
Confusing error when running ChIPQC
chipqc chipseq
updated 8.5 years ago by ▴ 420 • written 8.6 years ago by ★ 7.9k
3
votes
1
reply
1.1k
views
shiftApply verbosity (in ChIPQC)
ChIPQC s4vectors
updated 7.9 years ago by ▴ 420 • written 8.1 years ago by ▴ 140
0
votes
1
reply
2.0k
views
Error in ChIPQC: "Error in if (res >= minval) { : missing value where TRUE/FALSE needed"
chipqc
updated 7.9 years ago by ★ 5.1k • written 8.1 years ago by ▴ 140
0
votes
1
reply
1.3k
views
ChipQCSample error Error in `colnames<-`(`*tmp*`, value = c("A", "B", "C")) : length of 'dimnames' [2] not equal to array extent
chipseq chipqc
updated 8.0 years ago by ▴ 420 • written 8.0 years ago by • 0
1
vote
4
replies
1.5k
views
ChIPQC error: Error in generating sample data
ChIPQC
updated 7.9 years ago by ★ 5.1k • written 7.9 years ago by ▴ 30
3
votes
7
replies
2.3k
views
ChIPQC for a single sample (disabling facets)
ChipQc chipqc
7.8 years ago Coby Viner ▴ 50
4
votes
6
replies
2.0k
views
ChIPQC GRCh38 usage yields "Unsupported annotation:hg38"
chipqc ChIPQC
updated 7.6 years ago by ▴ 420 • written 7.6 years ago by ▴ 50
3
votes
6
replies
1.4k
views
ChIPQCreport yields a cryptic error if "Replicate" data is not specified
ChIPQC chipqc
updated 7.6 years ago by ★ 5.1k • written 7.6 years ago by ▴ 50
0
votes
4
replies
1.6k
views
ChIPQCreport Total number of duplicates differs from multiqc/fastqc & RelCC is Inf
ChIPQC ChIPQCreport
updated 6.9 years ago by ▴ 420 • written 6.9 years ago by ▴ 40
2
votes
5
replies
2.0k
views
ChIPQC gives Error subscript contains out-of-bounds ranges with custom transcript database
chipqc
updated 6.9 years ago by ▴ 420 • written 6.9 years ago by • 0
2
votes
1
reply
1.5k
views
ChIPQC with GRCh38/hg38 requires manual loading of hg38 annotation
chipqc
updated 6.8 years ago by ▴ 420 • written 6.9 years ago by ▴ 50
1
vote
2
replies
1.0k
views
ChIPQC report missing figures
chipqc software error
updated 6.8 years ago by ▴ 420 • written 6.8 years ago by ▴ 30
1
vote
3
replies
2.1k
views
ChipQC Error: first error: could not find function "seqlevels<-"
software error chipqc
6.8 years ago tirza.doniger ▴ 20
0
votes
1
reply
2.2k
views
Error computing metrics with ChIPQC (Bioconductor v3.5, ChIPQC v2.1.12)
chipqc chipqcreport
updated 6.8 years ago by ▴ 420 • written 6.8 years ago by • 0
0
votes
1
reply
2.6k
views
Unable to perform analysis on all the chromosomes with the latest version of ChIPQC 1.12
chipqc R
updated 6.8 years ago by ▴ 420 • written 6.8 years ago by • 0
0
votes
3
replies
1.6k
views
ChIPQC failed on chrM
ChIPQC
updated 6.8 years ago by ▴ 420 • written 6.8 years ago by • 0
0
votes
2
replies
1.0k
views
ChIPQC plots for input samples
chipqc
updated 6.8 years ago by ▴ 420 • written 6.8 years ago by ▴ 140
1
vote
1
reply
1.8k
views
ChIPQC bam and bed files question
chipqc
updated 6.8 years ago by ▴ 420 • written 6.8 years ago by • 0
0
votes
1
reply
2.0k
views
PCR bottleneck coefficient (PBC)
chipqc
updated 6.8 years ago by ★ 5.1k • written 6.8 years ago by ▴ 140
0
votes
3
replies
1.3k
views
ChiPQC run time error
ChiPQC
updated 6.7 years ago by ▴ 420 • written 6.7 years ago by • 0
0
votes
1
reply
1.5k
views
Can ChIPQC analyze mandarin duck ChIP-Seq data?
ChIPQC
updated 6.6 years ago by ▴ 420 • written 6.6 years ago by ▴ 20
0
votes
4
replies
2.2k
views
ChIPQC error: "non-zero exit status"
software error package installation chipqc txdb.hsapiens.ucsc.hg18.knowngene
updated 5.8 years ago by 25k • written 5.8 years ago by • 0
1
vote
7
replies
2.7k
views
ChipQC not loading files
ChipQC diffbind
updated 5.7 years ago by ▴ 420 • written 5.7 years ago by • 0
2
votes
2
replies
1.3k
views
ChIPQC gives Bam file has 297 contigs Error: subscript contains out-of-bounds indices
ChIP-seq ChIPQC QC
updated 4.7 years ago by ▴ 20 • written 5.2 years ago by ▴ 10
0
votes
1
reply
851
views
ChIPQC: Error in summary.factor
ChIPQC
updated 4.4 years ago by • 0 • written 4.5 years ago by • 0
0
votes
7
replies
1.8k
views
CHIPQC error regarding BiocParallel
CHIPQC Diffbind chipseq rory stark Thomas Carroll
updated 20 months ago by ▴ 40 • written 4.0 years ago by ▴ 10
2
votes
7
replies
1.9k
views
How to generate custom annotation for rat genome rn6 in ChIPQC
ChIPQC annotation rn6
updated 3 months ago by • 0 • written 3.6 years ago by • 0
0
votes
2
replies
1.7k
views
ChipQC 'names' attribute [9] must be the same length as the vector [2]'
chipqc
updated 3.2 years ago by • 0 • written 3.5 years ago by ▴ 40
50 results • Page 1 of 1
Recent ...
Replies
Comment: Memory errors using read.bismark? by Juan Higareda • 0
Thanks for the answer. Actually, processing one file and keeping it in memory wasn't the problem, is more processing all the 15 files to bu…
Answer: Differentially expressed genes in monocle pseudotime by Gordon Smyth 50k
You might try the methods in this paper: Cheng J, Smyth GK*, Chen Y* (2023). Unraveling the timeline of gene expression: A pseudotempora…
Comment: DESeq2 a lot of genes showing up as differentially expressed that only have 1 sa by Seyram M. • 0
Thank you Michael for your attention to my question. I am truly grateful. I subsetted the data using lines of codes to include only the g…
Comment: [DiffBind] Obtaining normalization factors by Henry ▴ 10
I see, thank you for your suggestion! I managed to use a separate RLE normalization to obtain the size factors.
Answer: Memory errors using read.bismark? by Peter Hickey ▴ 690
Thanks for sharing an example file. This is a very large non-CpG methylation dataset, which are tricky to work with for a number of reason…
Votes
Comment: [DiffBind] Obtaining normalization factors
Answer: ComplexHeatmap: add pch to rowAnnotation when the input is a data frame with var
Comment: Not fully paired differential gene expression analysis
Answer: GSVA error
Comment: DESeq2 - Plot Nr. Genes vs Variance explained in PCA
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