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hic
•
reset
0
votes
0
replies
536
views
hichip fragments extraction chip seq
ChIPSeqData
interact
GenomicRanges
HiC
15 months ago
user_bioinfo
• 0
0
votes
2
replies
781
views
Java error while running HiCDC overview code
JuicerTools
HiC
HiCDCPlus
Java
Juicer
written 2.0 years ago by
IsMM
• 0
0
votes
0
replies
1.3k
views
Job:
Bioinformatics Research Scientist- Epigenetics Group
HiC
Epigenetics
HiCHIP
ChIPSeq
3.5 years ago
xubeisi
• 0
0
votes
0
replies
1.5k
views
How to prepare HiCUP BAM output as input for HOMER?
HOMER
HiCUP
BAM
HiC
4.0 years ago
Ankit
▴ 20
0
votes
3
replies
1.3k
views
HiCDCPlus / HiC-DC+ is not found
HiCDCPlus
HiC-DC+
HiCcompare
HiC
updated 3.6 years ago by
merve.sahn
• 0 • written 5.1 years ago by
mtS
• 0
0
votes
0
replies
916
views
Looking for a package to efficiently plot Hi-C contact maps
HiC
hicrep
HiCcompare
5.1 years ago
changxu.fan
▴ 20
1
vote
7
replies
2.3k
views
problem recasting InteractionSet into a DGEList
diffHic
GenomicInteractions
edgeR
HiC
cooler
updated 5.3 years ago by
Aaron Lun
★ 29k • written 5.3 years ago by
Marco Blanchette
▴ 30
0
votes
1
reply
1.3k
views
How to load counts from existing count matrices in diffHic package
diffHic
HiC
InteractionSet
updated 5.6 years ago by
Aaron Lun
★ 29k • written 5.6 years ago by
girardot
• 0
0
votes
1
reply
1.3k
views
.cool to .txt cooler2bedpe does not work HiCompare
HiCompare
HiC
cool
updated 6.2 years ago by
Kevin Blighe
★ 4.0k • written 6.2 years ago by
c.chakraborty
• 0
0
votes
3
replies
2.1k
views
extracting scaffoldnames from HiC contact matrix
hic
updated 6.9 years ago by
bioparticles.melly
• 0 • written 6.9 years ago by
m.t.lorenc
• 0
0
votes
9
replies
2.3k
views
from denove contig assembly to chromosome bins
diffhic
gothic
hicup
hic-c
hic
updated 7.0 years ago by
Aaron Lun
★ 29k • written 7.0 years ago by
mictadlo
▴ 10
0
votes
1
reply
1.3k
views
Error in scanBam(bam_fn) : could not find function "scanBam"
hic
diffhic
gothic
hicup
hic-c
7.0 years ago
mictadlo
▴ 10
1
vote
1
reply
2.0k
views
extract HiC contacts for a given BEDPE set of coordinates
hic
diffhic
chromatin
bedpe
updated 7.3 years ago by
Aaron Lun
★ 29k • written 7.3 years ago by
gryderart
• 0
2
votes
1
reply
1.7k
views
Inflating interactionSets into a contact matrix
diffhic
hic
interactionset
contactmatrix
inflate
updated 8.1 years ago by
Aaron Lun
★ 29k • written 8.1 years ago by
hwick1
▴ 20
0
votes
8
replies
2.3k
views
How to get specific fragment/read interactions from HiC (diffHiC) data?
diffhic
hic
updated 8.1 years ago by
Aaron Lun
★ 29k • written 8.1 years ago by
hwick1
▴ 20
2
votes
2
replies
1.9k
views
Extracting non-interacting hic reads to create a sam/bam file
diffhic
hicpro
hic
8.3 years ago
sergio.espeso-gil
• 0
0
votes
3
replies
2.1k
views
GOTHiC hg19 error
GOTHiC
hic
10.2 years ago
Nathan Sheffield
▴ 10
4
votes
20
replies
3.5k
views
scaling loess curves
HiTC
gothic
diffhic
HiC
10.3 years ago • updated 10.2 years ago
Bogdan
▴ 670
18 results • Page
1 of 1
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Answer: PTM analysis in LIMPA
by
Gordon Smyth
53k
For PTM analysis, the usual quantification command dpcQuant() is replaced by dpcImpute(). Otherwise the limpa pipeline is the same as for a…
Answer: problem reading bam files into nucleR
by
James W. MacDonald
68k
The first step is to update to the current versions of R/Bioconductor and try again. It's possible that you have run into a bug that's alre…
Answer: Question about DESeq2 Design for Paired Treatment Study
by
ATpoint
★ 5.0k
It's a paired analysis so you don't need any patient-specific covariates such as age and sex. What you call batch effect might just be the …
Comment: problem reading bam files into nucleR
by
efoss
▴ 10
I thought I might be able to track down a problematic line in the bam file by repeatedly splitting the bam file in and then running the co…
Answer: two questions about limma
by
Gordon Smyth
53k
Answered here: https://support.bioconductor.org/p/16318/
Votes
C: DESeq2 Following RSEM
Upcoming Ensembl API and data access changes - new blog post available
Comment: Highly similar RNA-seq samples in PCA - pooling or technical duplication?
Answer: Large logFC but somewhat high FDR
Comment: upstream git branches of bioc-release
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68k
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