Showing : ChIPQC • reset
1
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ChipQC Error: first error: could not find function "seqlevels<-"
software error chipqc
8.3 years ago tirza.doniger ▴ 20
0
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1
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2.3k
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PCR bottleneck coefficient (PBC)
chipqc
updated 8.3 years ago by ★ 5.2k • written 8.3 years ago by ▴ 140
1
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1
reply
2.3k
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ChIPQC bam and bed files question
chipqc
updated 8.3 years ago by ▴ 420 • written 8.3 years ago by • 0
0
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2
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1.4k
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ChIPQC plots for input samples
chipqc
updated 8.3 years ago by ▴ 420 • written 8.3 years ago by ▴ 140
0
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3
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1.6k
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ChIPQC reading more samples that it should
chipqc
8.3 years ago C T ▴ 140
1
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3
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1.6k
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ChIPQC : ChIPQCreport(dba_object) getting error when drawing plotFribl
ChIPQC
8.3 years ago ZheFrench ▴ 60
0
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1
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2.9k
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Unable to perform analysis on all the chromosomes with the latest version of ChIPQC 1.12
chipqc R
updated 8.3 years ago by ▴ 420 • written 8.4 years ago by • 0
0
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3
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2.0k
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ChIPQC failed on chrM
ChIPQC
updated 8.3 years ago by ▴ 420 • written 8.4 years ago by • 0
0
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1
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2.6k
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Error computing metrics with ChIPQC (Bioconductor v3.5, ChIPQC v2.1.12)
chipqc chipqcreport
updated 8.4 years ago by ▴ 420 • written 8.4 years ago by • 0
1
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3
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1.5k
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ChIPQC installation does not force latest DiffBind version
chipqc diffbind chipqcreport
updated 8.4 years ago by ▴ 420 • written 8.4 years ago by ▴ 50
1
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2
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1.4k
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ChIPQC report missing figures
chipqc software error
updated 8.4 years ago by ▴ 420 • written 8.4 years ago by ▴ 30
2
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1
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2.0k
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ChIPQC with GRCh38/hg38 requires manual loading of hg38 annotation
chipqc
updated 8.4 years ago by ▴ 420 • written 8.4 years ago by ▴ 50
2
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5
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2.7k
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ChIPQC gives Error subscript contains out-of-bounds ranges with custom transcript database
chipqc
updated 8.4 years ago by ▴ 420 • written 8.4 years ago by • 0
0
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4
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2.2k
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ChIPQCreport Total number of duplicates differs from multiqc/fastqc & RelCC is Inf
ChIPQC ChIPQCreport
updated 8.4 years ago by ▴ 420 • written 8.4 years ago by ▴ 60
4
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2
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1.7k
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ChIPQC : ChIPQCreport(experiment) swap memory overload
ChIPQC ChIPQCreport
updated 8.4 years ago by ▴ 420 • written 8.4 years ago by ▴ 60
0
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0
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1.0k
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ChIPQC comparison of controls - uniqueness error
chipqc
8.4 years ago Coby Viner ▴ 50
2
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5
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2.1k
views
Error involving ChIPQCreport
ChIPQC
updated 8.6 years ago by ▴ 420 • written 8.6 years ago by • 0
0
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4
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1.8k
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ChIPQC plotCoverageHist() and plotCC() not showing inputs
ChIPQC plotCoverageHist plotCC input
8.8 years ago atisou • 0
0
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0
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950
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ChIPQC plotSSD adds a legend even without a blacklist [minor]
chipqc ChIPQC
9.1 years ago Coby Viner ▴ 50
3
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4
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1.8k
views
ChIPQC on samples without peaks and wrong total reads
chipqc
updated 9.1 years ago by ▴ 420 • written 9.1 years ago by ▴ 10
3
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6
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1.9k
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ChIPQCreport yields a cryptic error if "Replicate" data is not specified
ChIPQC chipqc
updated 9.1 years ago by ★ 5.2k • written 9.1 years ago by ▴ 50
4
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6
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2.7k
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ChIPQC GRCh38 usage yields "Unsupported annotation:hg38"
chipqc ChIPQC
updated 9.1 years ago by ▴ 420 • written 9.1 years ago by ▴ 50
0
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3
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1.7k
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Problems with double read counts on ChIPQC
chipqc
updated 9.1 years ago by • 0 • written 9.2 years ago by • 0
1
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2
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3.3k
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'reached elapsed time limit' error on ChIPQC
ChIPQC
updated 9.3 years ago by 25k • written 9.3 years ago by • 0
5
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3
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2.4k
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ChIPQC error: "if (nrow(pv$binding) > 0) { : argument is of length zero"
chipqc
9.3 years ago Danielle Denisko ▴ 30
3
votes
7
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3.1k
views
ChIPQC for a single sample (disabling facets)
ChipQc chipqc
9.3 years ago Coby Viner ▴ 50
1
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4
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2.0k
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ChIPQC error: Error in generating sample data
ChIPQC
updated 9.5 years ago by ★ 5.2k • written 9.5 years ago by ▴ 30
0
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1
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2.3k
views
Error in ChIPQC: "Error in if (res >= minval) { : missing value where TRUE/FALSE needed"
chipqc
updated 9.5 years ago by ★ 5.2k • written 9.7 years ago by ▴ 140
3
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1
reply
1.4k
views
shiftApply verbosity (in ChIPQC)
ChIPQC s4vectors
updated 9.5 years ago by ▴ 420 • written 9.7 years ago by ▴ 140
0
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1
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1.6k
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ChipQCSample error Error in `colnames<-`(`*tmp*`, value = c("A", "B", "C")) : length of 'dimnames' [2] not equal to array extent
chipseq chipqc
updated 9.5 years ago by ▴ 420 • written 9.5 years ago by • 0
4
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8
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2.9k
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ChIPQC and/or Diffbind - retrieving normalized read counts for peaks from single sample
DiffBind ChIPQC
9.7 years ago JD ▴ 10
4
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2
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2.2k
views
Confusing error when running ChIPQC
chipqc chipseq
updated 10.1 years ago by ▴ 420 • written 10.1 years ago by ★ 7.9k
3
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9
replies
3.9k
views
ChIPQC and broadPeak input
chipseq chipqc chip-seq
10.2 years ago • updated 10.1 years ago lindahove ▴ 10
0
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0
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1.2k
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ChIPQC showed errors 'nnodes' must be >= 1
software error bioconductor chipseq chipqc
10.2 years ago wangzhe335 • 0
3
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1
reply
3.9k
views
creating custom genome annotation for the ChIPQC package
ChIPSeq QC ChIPQC
updated 10.2 years ago by ▴ 420 • written 10.2 years ago by ▴ 160
4
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8
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3.1k
views
ChIPQC v1.4 fails uninformatively where version 1.2 works fine
chipqc
updated 10.3 years ago by ★ 5.2k • written 10.5 years ago by ▴ 140
1
vote
4
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2.7k
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ChIPQC: reads counts in bam do not match ones from samtools flagstat
chipqc
updated 10.6 years ago by ▴ 420 • written 10.6 years ago by • 0
0
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2
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3.9k
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Problem loading bamfiles to ChIPQC
ChIPQC
10.8 years ago sergio.espeso-gil • 0
0
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4
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2.2k
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ChiPQC and paired-end data
ChIPQC ChIPQC
updated 11.3 years ago by ▴ 20 • written 11.3 years ago by ▴ 340
89 results • Page 2 of 2
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Replies
Comment: deseq2 filter the low counts by Michael Love 43k
Have you seen this part: https://bioconductor.org/packages/release/bioc/vignettes/DESeq2/inst/doc/DESeq2.html#pre-filtering
Comment: deseq2 filter the low counts by empty_mt • 0
Hi Michael, My matrix consists of 36 samples from 6 treatments (6 samples/ treatment), whether I adjust prefiltering parameters or not, in…
Comment: Best practice for handling large data (matrix with >2^31-1 non-zero elements) in by dan.gatti • 0
That works. I didn't realize what you said about HDF5 files. We always keep those and archive the MTX files. I'm able to read in the file…
Comment: DESeq2 interactions by Michael Love 43k
GPT even v4 gives pretty good answers to DESeq2 questions that are similar to those already posted on the support site. I've also noticed …
Answer: Important: Bioconductor Release 3.22 Delayed by shepherl 4.2k
We will continue with the release on Thursday October 30th. We have shifted one day as originally planned. Thank you
Votes
Answer: DESeq2 interactions
Answer: Important: Bioconductor Release 3.22 Delayed
A: Multi-level experiments in Limma
Answer: Should voomWithQualityWeights still be used when the sample-specific weights var
Answer: DESeq2 for candidate gene analysis
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