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Showing :
ChipQC
•
reset
5
votes
3
replies
1.4k
views
ChIPQC error: "if (nrow(pv$binding) > 0) { : argument is of length zero"
chipqc
5.8 years ago
Danielle Denisko
▴ 30
5
votes
11
replies
1.2k
views
ChIPQC Error in .Call2 NCList object is too deep
ChIPQC
updated 4.5 years ago by
Thomas Carroll
▴ 400 • written 4.5 years ago by
Victor Goitea
▴ 10
4
votes
8
replies
1.7k
views
ChIPQC v1.4 fails uninformatively where version 1.2 works fine
chipqc
updated 6.9 years ago by
Rory Stark
★ 4.4k • written 7.1 years ago by
liz.ingsimmons
▴ 140
4
votes
2
replies
1.3k
views
Confusing error when running ChIPQC
chipqc
chipseq
updated 6.6 years ago by
Thomas Carroll
▴ 400 • written 6.6 years ago by
Ryan C. Thompson
7.8k
4
votes
6
replies
1.2k
views
ChIPQC GRCh38 usage yields "Unsupported annotation:hg38"
chipqc
ChIPQC
updated 5.7 years ago by
Thomas Carroll
▴ 400 • written 5.7 years ago by
Coby Viner
▴ 50
4
votes
8
replies
1.6k
views
ChIPQC and/or Diffbind - retrieving normalized read counts for peaks from single sample
DiffBind
ChIPQC
6.3 years ago
JD
▴ 10
4
votes
2
replies
844
views
ChIPQC : ChIPQCreport(experiment) swap memory overload
ChIPQC
ChIPQCreport
updated 5.0 years ago by
Thomas Carroll
▴ 400 • written 5.0 years ago by
ZheFrench
▴ 30
3
votes
9
replies
2.0k
views
ChIPQC and broadPeak input
chipseq
chipqc
chip-seq
6.7 years ago
lindahove
▴ 10
3
votes
6
replies
1.0k
views
Integer overflow issue with ChIPQC
ChIPQC
Rstudio
updated 2.8 years ago by
Martin Morgan
25k • written 2.8 years ago by
Nitesh Kumar Singh
▴ 30
3
votes
12
replies
2.7k
views
ChIPQC failling when run ChIPQC() over 6 samples
chipqc
updated 4.7 years ago by
Thomas Carroll
▴ 400 • written 7.2 years ago by
atisou
• 0
3
votes
1
reply
2.1k
views
creating custom genome annotation for the ChIPQC package
ChIPSeq
QC
ChIPQC
updated 6.8 years ago by
Thomas Carroll
▴ 400 • written 6.8 years ago by
Philip Lijnzaad
▴ 160
3
votes
6
replies
889
views
ChIPQCreport yields a cryptic error if "Replicate" data is not specified
ChIPQC
chipqc
updated 5.6 years ago by
Rory Stark
★ 4.4k • written 5.6 years ago by
Coby Viner
▴ 50
3
votes
1
reply
770
views
shiftApply verbosity (in ChIPQC)
ChIPQC
s4vectors
updated 6.0 years ago by
Thomas Carroll
▴ 400 • written 6.2 years ago by
liz.ingsimmons
▴ 140
3
votes
7
replies
1.5k
views
ChIPQC for a single sample (disabling facets)
ChipQc
chipqc
5.9 years ago
Coby Viner
▴ 50
3
votes
4
replies
844
views
ChIPQC on samples without peaks and wrong total reads
chipqc
updated 5.6 years ago by
Thomas Carroll
▴ 400 • written 5.7 years ago by
Amitha Sampath
▴ 10
2
votes
1
reply
897
views
ChIPQC with GRCh38/hg38 requires manual loading of hg38 annotation
chipqc
updated 4.9 years ago by
Thomas Carroll
▴ 400 • written 4.9 years ago by
Coby Viner
▴ 50
2
votes
5
replies
1.5k
views
ChIPQC - can't read in bam files
chipqc
chipqcreport
3.7 years ago
molly_the_minotaur
▴ 20
2
votes
5
replies
1.2k
views
Diffbind: dba.plot retrieve variance explained
diffbind
chipqc
updated 4.7 years ago by
Rory Stark
★ 4.4k • written 4.7 years ago by
ZheFrench
▴ 30
2
votes
6
replies
612
views
How to generate custom annotation for rat genome rn6 in ChIPQC
ChIPQC
annotation
rn6
20 months ago • updated 17 months ago
Frédéric Crémazy
• 0
2
votes
5
replies
1.3k
views
ChIPQC gives Error subscript contains out-of-bounds ranges with custom transcript database
chipqc
updated 5.0 years ago by
Thomas Carroll
▴ 400 • written 5.0 years ago by
tofukaj
• 0
2
votes
6
replies
1.4k
views
ChIPQC: error during annotation compilation
ChIPQC
updated 3.7 years ago by
Thomas Carroll
▴ 400 • written 3.7 years ago by
hdingwall
▴ 10
2
votes
5
replies
878
views
Error involving ChIPQCreport
ChIPQC
updated 5.1 years ago by
Thomas Carroll
▴ 400 • written 5.2 years ago by
Roger
• 0
2
votes
2
replies
806
views
ChIPQC gives Bam file has 297 contigs Error: subscript contains out-of-bounds indices
ChIP-seq
ChIPQC
QC
updated 2.8 years ago by
zhenfeng.liu1
▴ 20 • written 3.2 years ago by
star
▴ 10
2
votes
4
replies
1.7k
views
ChIPQC error: "names' attribute [9] must be the same length as the vector [7]"
ChIPQC
updated 9 months ago by
Yue
• 0 • written 2.9 years ago by
analeigh.gui
▴ 20
1
vote
3
replies
1.6k
views
Downsampling ChIP-seq BAM files with spike in normalization factor before feeding into Diffbind
diffbind
chipseq
chipqc
updated 18 months ago by
Rory Stark
★ 4.4k • written 4.2 years ago by
bioinfouser2
▴ 10
1
vote
5
replies
10.0k
views
Error: Faceting variables must have at least one value when plotting with ChIPQC
ChipQC
chipqc
updated 3 months ago by
Gopal
• 0 • written 5.7 years ago by
thekatybrown
▴ 10
1
vote
4
replies
1.6k
views
ChIPQC: reads counts in bam do not match ones from samtools flagstat
chipqc
updated 7.2 years ago by
Thomas Carroll
▴ 400 • written 7.2 years ago by
atisou
• 0
1
vote
4
replies
1.1k
views
ChIPQC error: Error in generating sample data
ChIPQC
updated 6.0 years ago by
Rory Stark
★ 4.4k • written 6.0 years ago by
meeta.mistry
▴ 20
1
vote
2
replies
653
views
ChIPQC report missing figures
chipqc
software error
updated 4.9 years ago by
Thomas Carroll
▴ 400 • written 4.9 years ago by
meeta.mistry
▴ 20
1
vote
3
replies
646
views
ChIPQC installation does not force latest DiffBind version
chipqc
diffbind
chipqcreport
updated 4.9 years ago by
Thomas Carroll
▴ 400 • written 4.9 years ago by
Coby Viner
▴ 50
1
vote
3
replies
1.3k
views
ChipQC Error: first error: could not find function "seqlevels<-"
software error
chipqc
4.8 years ago
tirza.doniger
▴ 20
1
vote
3
replies
629
views
ChIPQC : ChIPQCreport(dba_object) getting error when drawing plotFribl
ChIPQC
4.9 years ago
ZheFrench
▴ 30
1
vote
2
replies
2.1k
views
'reached elapsed time limit' error on ChIPQC
ChIPQC
updated 5.8 years ago by
Martin Morgan
25k • written 5.8 years ago by
cattapre
• 0
1
vote
7
replies
1.8k
views
ChipQC not loading files
ChipQC
diffbind
updated 3.7 years ago by
Thomas Carroll
▴ 400 • written 3.8 years ago by
avp25
• 0
1
vote
1
reply
246
views
ChIPQC 'Contigs of interest are not all in Bam file!!' error
ChIPQC
12 months ago
Jonah
• 0
1
vote
2
replies
267
views
ChIPQC: log2 or log10?
ChIPQC
10 months ago
etiennedanis
• 0
0
votes
1
reply
1.6k
views
Error computing metrics with ChIPQC (Bioconductor v3.5, ChIPQC v2.1.12)
chipqc
chipqcreport
updated 4.9 years ago by
Thomas Carroll
▴ 400 • written 4.9 years ago by
Roger
• 0
0
votes
1
reply
2.1k
views
Unable to perform analysis on all the chromosomes with the latest version of ChIPQC 1.12
chipqc
R
updated 4.9 years ago by
Thomas Carroll
▴ 400 • written 4.9 years ago by
tuteja.reetu
• 0
0
votes
3
replies
1.2k
views
ChIPQC failed on chrM
ChIPQC
updated 4.9 years ago by
Thomas Carroll
▴ 400 • written 4.9 years ago by
seasky002002
• 0
0
votes
3
replies
892
views
ChIPQC reading more samples that it should
chipqc
4.9 years ago
C T
▴ 140
0
votes
0
replies
141
views
ChIPQC: Theme
ChIPQC
10 months ago
etiennedanis
• 0
0
votes
2
replies
685
views
ChIPQC plots for input samples
chipqc
updated 4.9 years ago by
Thomas Carroll
▴ 400 • written 4.9 years ago by
C T
▴ 140
0
votes
1
reply
990
views
ChIPQC bam and bed files question
chipqc
updated 4.9 years ago by
Thomas Carroll
▴ 400 • written 4.9 years ago by
woongjaej
• 0
0
votes
1
reply
1.4k
views
PCR bottleneck coefficient (PBC)
chipqc
updated 4.9 years ago by
Rory Stark
★ 4.4k • written 4.9 years ago by
C T
▴ 140
0
votes
3
replies
787
views
ChiPQC run time error
ChiPQC
updated 4.8 years ago by
Thomas Carroll
▴ 400 • written 4.8 years ago by
NANADAWONG
• 0
0
votes
4
replies
1.0k
views
Unhelpful Errors Running ChIPQC on Computing Cluster
chipqc
chipqcreport
4.7 years ago
jared.andrews07
▴ 30
0
votes
1
reply
1.0k
views
ChipQCSample error Error in `colnames<-`(`*tmp*`, value = c("A", "B", "C")) : length of 'dimnames' [2] not equal to array extent
chipseq
chipqc
updated 6.1 years ago by
Thomas Carroll
▴ 400 • written 6.1 years ago by
ssn4ssn
• 0
0
votes
1
reply
793
views
Can ChIPQC analyze mandarin duck ChIP-Seq data?
ChIPQC
updated 4.6 years ago by
Thomas Carroll
▴ 400 • written 4.7 years ago by
Gary
▴ 20
0
votes
0
replies
526
views
ChIPQC stops at chr3 for calculating shift
chipqc
4.7 years ago
psudyant
• 0
0
votes
0
replies
747
views
ChIPQC: Error in names(res) <- nms
ChIPQC
chip-seq
4.5 years ago
nbkingsley
• 0
50 results • Page
1 of 1
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Comment: TPM data Differential expression analysis
by
hnthirim
▴ 10
Hi @gordonsmyth, Question on your above answer: I have logTPM normalized data. Can I perform DE analysis using it on EdgeR, instead of in…
Comment: rtracklayer S.h
by
gibran
• 0
Thanks, much appreciated. So I think this approach actually gets binaries and I'm not sure how to isolate the problem I was experiencing as…
Comment: DESeq2, Calculate the size factor by using median-of-ratio
by
KEREN
• 0
Hi Michael, thank you for you reply. My concern here mainly focus on the high variances in samples of condition "mESC_mRNA_WT". I observed…
Comment: DiffBind: 0 consensus peaks for dba.peakset: New bug / undocumented change intro
by
Rory Stark
★ 4.4k
I agree the documentation could be clearer -- it took me a while to understand what it said so I could address your issue!
Answer: DiffBind: 0 consensus peaks for dba.peakset: New bug / undocumented change intro
by
chrarnold
• 0
Thanks a lot for your quick reply, it is very appreciated! Indeed, with your 2 suggested modifications, I can again reproduce the results f…
Votes
Answer: rtracklayer S.h
Answer: rtracklayer S.h
Answer: DESeq2: Extracting Averaged Counts Information from dds and rld
Answer: DESeq2: Extracting Averaged Counts Information from dds and rld
Answer: DESeq2: Extracting Averaged Counts Information from dds and rld
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