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CHIPQC
•
reset
1
vote
3
replies
2.6k
views
ChipQC Error: first error: could not find function "seqlevels<-"
software error
chipqc
8.3 years ago
tirza.doniger
▴ 20
0
votes
1
reply
2.3k
views
PCR bottleneck coefficient (PBC)
chipqc
updated 8.3 years ago by
Rory Stark
★ 5.2k • written 8.3 years ago by
C T
▴ 140
1
vote
1
reply
2.3k
views
ChIPQC bam and bed files question
chipqc
updated 8.3 years ago by
Thomas Carroll
▴ 420 • written 8.3 years ago by
woongjaej
• 0
0
votes
2
replies
1.4k
views
ChIPQC plots for input samples
chipqc
updated 8.3 years ago by
Thomas Carroll
▴ 420 • written 8.3 years ago by
C T
▴ 140
0
votes
3
replies
1.6k
views
ChIPQC reading more samples that it should
chipqc
8.3 years ago
C T
▴ 140
1
vote
3
replies
1.6k
views
ChIPQC : ChIPQCreport(dba_object) getting error when drawing plotFribl
ChIPQC
8.3 years ago
ZheFrench
▴ 60
0
votes
1
reply
2.9k
views
Unable to perform analysis on all the chromosomes with the latest version of ChIPQC 1.12
chipqc
R
updated 8.3 years ago by
Thomas Carroll
▴ 420 • written 8.4 years ago by
tuteja.reetu
• 0
0
votes
3
replies
2.0k
views
ChIPQC failed on chrM
ChIPQC
updated 8.3 years ago by
Thomas Carroll
▴ 420 • written 8.3 years ago by
seasky002002
• 0
0
votes
1
reply
2.6k
views
Error computing metrics with ChIPQC (Bioconductor v3.5, ChIPQC v2.1.12)
chipqc
chipqcreport
updated 8.4 years ago by
Thomas Carroll
▴ 420 • written 8.4 years ago by
Roger
• 0
1
vote
3
replies
1.5k
views
ChIPQC installation does not force latest DiffBind version
chipqc
diffbind
chipqcreport
updated 8.4 years ago by
Thomas Carroll
▴ 420 • written 8.4 years ago by
Coby Viner
▴ 50
1
vote
2
replies
1.4k
views
ChIPQC report missing figures
chipqc
software error
updated 8.4 years ago by
Thomas Carroll
▴ 420 • written 8.4 years ago by
meeta.mistry
▴ 30
2
votes
1
reply
2.0k
views
ChIPQC with GRCh38/hg38 requires manual loading of hg38 annotation
chipqc
updated 8.4 years ago by
Thomas Carroll
▴ 420 • written 8.4 years ago by
Coby Viner
▴ 50
2
votes
5
replies
2.7k
views
ChIPQC gives Error subscript contains out-of-bounds ranges with custom transcript database
chipqc
updated 8.4 years ago by
Thomas Carroll
▴ 420 • written 8.4 years ago by
tofukaj
• 0
0
votes
4
replies
2.1k
views
ChIPQCreport Total number of duplicates differs from multiqc/fastqc & RelCC is Inf
ChIPQC
ChIPQCreport
updated 8.4 years ago by
Thomas Carroll
▴ 420 • written 8.4 years ago by
ZheFrench
▴ 60
4
votes
2
replies
1.7k
views
ChIPQC : ChIPQCreport(experiment) swap memory overload
ChIPQC
ChIPQCreport
updated 8.4 years ago by
Thomas Carroll
▴ 420 • written 8.4 years ago by
ZheFrench
▴ 60
0
votes
0
replies
1.0k
views
ChIPQC comparison of controls - uniqueness error
chipqc
8.4 years ago
Coby Viner
▴ 50
2
votes
5
replies
2.1k
views
Error involving ChIPQCreport
ChIPQC
updated 8.6 years ago by
Thomas Carroll
▴ 420 • written 8.6 years ago by
Roger
• 0
0
votes
4
replies
1.8k
views
ChIPQC plotCoverageHist() and plotCC() not showing inputs
ChIPQC
plotCoverageHist
plotCC
input
8.7 years ago
atisou
• 0
0
votes
0
replies
946
views
ChIPQC plotSSD adds a legend even without a blacklist [minor]
chipqc
ChIPQC
9.1 years ago
Coby Viner
▴ 50
3
votes
4
replies
1.8k
views
ChIPQC on samples without peaks and wrong total reads
chipqc
updated 9.1 years ago by
Thomas Carroll
▴ 420 • written 9.1 years ago by
Amitha Sampath
▴ 10
3
votes
6
replies
1.9k
views
ChIPQCreport yields a cryptic error if "Replicate" data is not specified
ChIPQC
chipqc
updated 9.1 years ago by
Rory Stark
★ 5.2k • written 9.1 years ago by
Coby Viner
▴ 50
4
votes
6
replies
2.7k
views
ChIPQC GRCh38 usage yields "Unsupported annotation:hg38"
chipqc
ChIPQC
updated 9.1 years ago by
Thomas Carroll
▴ 420 • written 9.1 years ago by
Coby Viner
▴ 50
0
votes
3
replies
1.7k
views
Problems with double read counts on ChIPQC
chipqc
updated 9.1 years ago by
rsuarez
• 0 • written 9.1 years ago by
cattapre
• 0
1
vote
2
replies
3.3k
views
'reached elapsed time limit' error on ChIPQC
ChIPQC
updated 9.3 years ago by
Martin Morgan
25k • written 9.3 years ago by
cattapre
• 0
5
votes
3
replies
2.4k
views
ChIPQC error: "if (nrow(pv$binding) > 0) { : argument is of length zero"
chipqc
9.3 years ago
Danielle Denisko
▴ 30
3
votes
7
replies
3.1k
views
ChIPQC for a single sample (disabling facets)
ChipQc
chipqc
9.3 years ago
Coby Viner
▴ 50
1
vote
4
replies
2.0k
views
ChIPQC error: Error in generating sample data
ChIPQC
updated 9.4 years ago by
Rory Stark
★ 5.2k • written 9.4 years ago by
meeta.mistry
▴ 30
0
votes
1
reply
2.3k
views
Error in ChIPQC: "Error in if (res >= minval) { : missing value where TRUE/FALSE needed"
chipqc
updated 9.4 years ago by
Rory Stark
★ 5.2k • written 9.6 years ago by
liz.ingsimmons
▴ 140
3
votes
1
reply
1.4k
views
shiftApply verbosity (in ChIPQC)
ChIPQC
s4vectors
updated 9.4 years ago by
Thomas Carroll
▴ 420 • written 9.6 years ago by
liz.ingsimmons
▴ 140
0
votes
1
reply
1.6k
views
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
Thomas Carroll
▴ 420 • written 9.5 years ago by
ssn4ssn
• 0
4
votes
8
replies
2.9k
views
ChIPQC and/or Diffbind - retrieving normalized read counts for peaks from single sample
DiffBind
ChIPQC
9.7 years ago
JD
▴ 10
4
votes
2
replies
2.2k
views
Confusing error when running ChIPQC
chipqc
chipseq
updated 10.1 years ago by
Thomas Carroll
▴ 420 • written 10.1 years ago by
Ryan C. Thompson
★ 7.9k
3
votes
9
replies
3.8k
views
ChIPQC and broadPeak input
chipseq
chipqc
chip-seq
10.1 years ago
lindahove
▴ 10
0
votes
0
replies
1.2k
views
ChIPQC showed errors 'nnodes' must be >= 1
software error
bioconductor
chipseq
chipqc
10.2 years ago
wangzhe335
• 0
3
votes
1
reply
3.9k
views
creating custom genome annotation for the ChIPQC package
ChIPSeq
QC
ChIPQC
updated 10.2 years ago by
Thomas Carroll
▴ 420 • written 10.2 years ago by
Philip Lijnzaad
▴ 160
4
votes
8
replies
3.1k
views
ChIPQC v1.4 fails uninformatively where version 1.2 works fine
chipqc
updated 10.3 years ago by
Rory Stark
★ 5.2k • written 10.5 years ago by
liz.ingsimmons
▴ 140
1
vote
4
replies
2.7k
views
ChIPQC: reads counts in bam do not match ones from samtools flagstat
chipqc
updated 10.6 years ago by
Thomas Carroll
▴ 420 • written 10.6 years ago by
atisou
• 0
0
votes
2
replies
3.9k
views
Problem loading bamfiles to ChIPQC
ChIPQC
10.8 years ago
sergio.espeso-gil
• 0
0
votes
4
replies
2.2k
views
ChiPQC and paired-end data
ChIPQC
ChIPQC
updated 11.2 years ago by
Carroll, Thomas
▴ 20 • written 11.3 years ago by
Ugo Borello
▴ 340
89 results • Page
2 of 2
Recent ...
Replies
Comment: Best practice for handling large data (matrix with >2^31-1 non-zero elements) in
by
James W. MacDonald
68k
Did you use the development version as Aaron suggested? There is an argument to read the market matrix file directly into an `SVT_SparseMat…
Comment: Best practice for handling large data (matrix with >2^31-1 non-zero elements) in
by
dan.gatti
• 0
Was anyone else able to put the pieces together using the reply above? I read in one 10X sample using DropletUtils::read10xCounts() and thi…
Comment: Announcing GBCC 2025: The first-ever joint conference between Bioconductor and G
by
dzv20413
• 0
Wow, GBCC 2025 sounds amazing, can not wait to see the logo contest results! Also, I just played [Level Devil][1] and it is super addictive…
Comment: Memory error while running alignments
by
Erik Wright
▴ 150
How much memory is available on the computer? A distance matrix of 50k sequences requires at least 50k*50k/2 * 8 bytes = 10GB, assuming the…
Comment: NA values for DESeq2 p-values and adjusted p-values using large sample sizes
by
Gabriel
• 0
Thank you very much for the reply. However, none of these three options seems to fit: 1) The genes for which NA appears do not have all 0 …
Votes
Comment: Check removeBatchEffect effectiveness
Comment: Streamlining the computing time for MiloDE p-value correction in large dataset?
Answer: DESeq2 design for haplotype MPRA
A: Different logFC (log2foldchange) values for genes from limma-voom and other too
Comment: Check removeBatchEffect effectiveness
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