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Showing :
HiC
•
reset
0
votes
0
replies
362
views
hichip fragments extraction chip seq
ChIPSeqData
interact
GenomicRanges
HiC
8 months ago
user_bioinfo
• 0
0
votes
2
replies
623
views
Java error while running HiCDC overview code
JuicerTools
HiC
HiCDCPlus
Java
Juicer
written 16 months ago by
IsMM
• 0
0
votes
0
replies
1.1k
views
Job:
Bioinformatics Research Scientist- Epigenetics Group
HiC
Epigenetics
HiCHIP
ChIPSeq
2.9 years ago
xubeisi
• 0
0
votes
0
replies
1.2k
views
How to prepare HiCUP BAM output as input for HOMER?
HOMER
HiCUP
BAM
HiC
3.4 years ago
Ankit
▴ 20
0
votes
3
replies
1.1k
views
HiCDCPlus / HiC-DC+ is not found
HiCDCPlus
HiC-DC+
HiCcompare
HiC
updated 3.0 years ago by
merve.sahn
• 0 • written 4.5 years ago by
mtS
• 0
0
votes
0
replies
776
views
Looking for a package to efficiently plot Hi-C contact maps
HiC
hicrep
HiCcompare
4.5 years ago
changxu.fan
▴ 20
1
vote
7
replies
2.0k
views
problem recasting InteractionSet into a DGEList
diffHic
GenomicInteractions
edgeR
HiC
cooler
updated 4.7 years ago by
Aaron Lun
★ 28k • written 4.7 years ago by
Marco Blanchette
▴ 30
0
votes
1
reply
1.2k
views
How to load counts from existing count matrices in diffHic package
diffHic
HiC
InteractionSet
updated 5.0 years ago by
Aaron Lun
★ 28k • written 5.0 years ago by
girardot
• 0
0
votes
1
reply
1.2k
views
.cool to .txt cooler2bedpe does not work HiCompare
HiCompare
HiC
cool
updated 5.6 years ago by
Kevin Blighe
★ 4.0k • written 5.6 years ago by
c.chakraborty
• 0
0
votes
3
replies
1.9k
views
extracting scaffoldnames from HiC contact matrix
hic
updated 6.3 years ago by
bioparticles.melly
• 0 • written 6.3 years ago by
m.t.lorenc
• 0
0
votes
9
replies
2.0k
views
from denove contig assembly to chromosome bins
diffhic
gothic
hicup
hic-c
hic
updated 6.4 years ago by
Aaron Lun
★ 28k • written 6.4 years ago by
mictadlo
▴ 10
0
votes
1
reply
1.2k
views
Error in scanBam(bam_fn) : could not find function "scanBam"
hic
diffhic
gothic
hicup
hic-c
6.4 years ago
mictadlo
▴ 10
1
vote
1
reply
1.8k
views
extract HiC contacts for a given BEDPE set of coordinates
hic
diffhic
chromatin
bedpe
updated 6.7 years ago by
Aaron Lun
★ 28k • written 6.7 years ago by
gryderart
• 0
2
votes
1
reply
1.5k
views
Inflating interactionSets into a contact matrix
diffhic
hic
interactionset
contactmatrix
inflate
updated 7.5 years ago by
Aaron Lun
★ 28k • written 7.5 years ago by
hwick1
▴ 20
0
votes
8
replies
2.1k
views
How to get specific fragment/read interactions from HiC (diffHiC) data?
diffhic
hic
updated 7.5 years ago by
Aaron Lun
★ 28k • written 7.5 years ago by
hwick1
▴ 20
2
votes
2
replies
1.7k
views
Extracting non-interacting hic reads to create a sam/bam file
diffhic
hicpro
hic
7.7 years ago
sergio.espeso-gil
• 0
0
votes
3
replies
1.9k
views
GOTHiC hg19 error
GOTHiC
hic
9.6 years ago
Nathan Sheffield
▴ 10
4
votes
20
replies
3.2k
views
scaling loess curves
HiTC
gothic
diffhic
HiC
9.6 years ago
Bogdan
▴ 670
18 results • Page
1 of 1
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Replies
Comment: error in ChAMP loading file
by
janwilseo
• 0
Any update on this post? I also had an issue with this. [erosion control](https://charlestonhydroseeding.com/)
Answer: CluserProfiler message "No gene can be mapped"
by
James W. MacDonald
68k
Two things. First, the order of your term2gene is backwards (should be term and then gene, like the name), and by default `enricher` adjust…
Comment: Controlling for batch and estrus cycle using DESeq2 in RNA-seq analysis
by
donnycrimson
• 0
One potential workaround might be to adjust for these factors using a combination of design matrices perhaps including batch as a covariate…
Comment: DESeq2 Design controlling for gender
by
donnycrimson
• 0
On a lighter note, while you are tackling such complex data, you might enjoy a quick break playing the [Slope Game](https://slopegame.lol)…
Comment: MetaDE.pvalue: Error in xj[i]: invalid subscript type 'list'
by
donnycrimson
• 0
Have you considered streamlining how you handle data input to mitigate these issues. It might help to define the parameters more strictly …
Votes
remove X and Y chromosome genes in RNA-seq data using DESeq2 pipeline
How to remove X & Y chromosome genes from RNAseq data
Is it advisable to remove X and Y chromosome genes in mouse bulk RNA-seq data at the level of the count matrix?
A: Unbalanced experiment with multiple samples from each patient.
A: Understanding contrasts limma
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