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Showing :
HiC
•
reset
0
votes
0
replies
291
views
hichip fragments extraction chip seq
ChIPSeqData
interact
GenomicRanges
HiC
5 months ago
user_bioinfo
• 0
0
votes
2
replies
543
views
Java error while running HiCDC overview code
JuicerTools
HiC
HiCDCPlus
Java
Juicer
written 14 months ago by
IsMM
• 0
0
votes
0
replies
1.0k
views
Job:
Bioinformatics Research Scientist- Epigenetics Group
HiC
Epigenetics
HiCHIP
ChIPSeq
2.6 years ago
xubeisi
• 0
0
votes
0
replies
1.1k
views
How to prepare HiCUP BAM output as input for HOMER?
HOMER
HiCUP
BAM
HiC
3.2 years ago
Ankit
▴ 20
0
votes
3
replies
1.0k
views
HiCDCPlus / HiC-DC+ is not found
HiCDCPlus
HiC-DC+
HiCcompare
HiC
updated 2.7 years ago by
merve.sahn
• 0 • written 4.2 years ago by
mtS
• 0
0
votes
0
replies
719
views
Looking for a package to efficiently plot Hi-C contact maps
HiC
hicrep
HiCcompare
4.3 years ago
changxu.fan
▴ 20
1
vote
7
replies
1.9k
views
problem recasting InteractionSet into a DGEList
diffHic
GenomicInteractions
edgeR
HiC
cooler
updated 4.4 years ago by
Aaron Lun
★ 28k • written 4.4 years ago by
Marco Blanchette
▴ 30
0
votes
1
reply
1.1k
views
How to load counts from existing count matrices in diffHic package
diffHic
HiC
InteractionSet
updated 4.8 years ago by
Aaron Lun
★ 28k • written 4.8 years ago by
girardot
• 0
0
votes
1
reply
1.1k
views
.cool to .txt cooler2bedpe does not work HiCompare
HiCompare
HiC
cool
updated 5.3 years ago by
Kevin Blighe
★ 4.0k • written 5.3 years ago by
c.chakraborty
• 0
0
votes
3
replies
1.8k
views
extracting scaffoldnames from HiC contact matrix
hic
updated 6.0 years ago by
bioparticles.melly
• 0 • written 6.1 years ago by
m.t.lorenc
• 0
0
votes
9
replies
1.8k
views
from denove contig assembly to chromosome bins
diffhic
gothic
hicup
hic-c
hic
updated 6.1 years ago by
Aaron Lun
★ 28k • written 6.1 years ago by
mictadlo
▴ 10
0
votes
1
reply
1.1k
views
Error in scanBam(bam_fn) : could not find function "scanBam"
hic
diffhic
gothic
hicup
hic-c
6.2 years ago • updated 6.1 years ago
mictadlo
▴ 10
1
vote
1
reply
1.7k
views
extract HiC contacts for a given BEDPE set of coordinates
hic
diffhic
chromatin
bedpe
updated 6.4 years ago by
Aaron Lun
★ 28k • written 6.4 years ago by
gryderart
• 0
2
votes
1
reply
1.5k
views
Inflating interactionSets into a contact matrix
diffhic
hic
interactionset
contactmatrix
inflate
updated 7.3 years ago by
Aaron Lun
★ 28k • written 7.3 years ago by
hwick1
▴ 20
0
votes
8
replies
1.9k
views
How to get specific fragment/read interactions from HiC (diffHiC) data?
diffhic
hic
updated 7.3 years ago by
Aaron Lun
★ 28k • written 7.3 years ago by
hwick1
▴ 20
2
votes
2
replies
1.6k
views
Extracting non-interacting hic reads to create a sam/bam file
diffhic
hicpro
hic
7.5 years ago
sergio.espeso-gil
• 0
0
votes
3
replies
1.9k
views
GOTHiC hg19 error
GOTHiC
hic
9.4 years ago
Nathan Sheffield
▴ 10
4
votes
20
replies
2.9k
views
scaling loess curves
HiTC
gothic
diffhic
HiC
9.4 years ago
Bogdan
▴ 670
18 results • Page
1 of 1
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Replies
Comment: input for singR function
by
iamin053
• 0
Hi Paria, I'm wondering if you were able to get an answer on this please. I would greatly appreciate any comments!
Comment: build samplesheet and plot profile
by
yf
• 0
![enter image description here][1] [1]: /media/images/8ea93bd0-bc90-443d-a332-4701f54a
Answer: I am having issues with bowtie2_build
by
James W. MacDonald
67k
Is proof.fa an actual FASTA file? Have you tried using the demo data that comes with the package? See the [vignette under Build Bowtie Inde…
Answer: DEG analysis across multiple timepoints, treatments and tissues
by
Michael Love
43k
Yes, if you think the entire time course can be modified by tissue effects then you would include another set of interaction terms. I re…
Comment: How to visualize these pathways using pathview
by
Guido Hooiveld
★ 4.1k
FYI: a similar, if not identical issue has been reported before (`pathview` has problems visualizing some pathways, but not all). You likel…
Votes
A: Doubt about the "zero expression" genes or genes with no reads at all in the co
Answer: Unable to install nloptr
Answer: ensembldb for Homo Sapiens organism containing superfluous SYMBOL genes?
C: How does edgeR cpm function calculate log(CPM) values?
Answer: Selection of correct coefficients or contrasts in DESeq2
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