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Showing :
HiC
•
reset
0
votes
2
replies
291
views
Java error while running HiCDC overview code
JuicerTools
HiC
HiCDCPlus
Java
Juicer
written 4 months ago by
IsMM
• 0
0
votes
0
replies
797
views
Job:
Bioinformatics Research Scientist- Epigenetics Group
HiC
Epigenetics
HiCHIP
ChIPSeq
22 months ago
xubeisi
• 0
0
votes
0
replies
811
views
How to prepare HiCUP BAM output as input for HOMER?
HOMER
HiCUP
BAM
HiC
2.4 years ago
Ankit
▴ 20
0
votes
3
replies
835
views
HiCDCPlus / HiC-DC+ is not found
HiCDCPlus
HiC-DC+
HiCcompare
HiC
updated 24 months ago by
merve.sahn
• 0 • written 3.5 years ago by
mtS
• 0
0
votes
0
replies
552
views
Looking for a package to efficiently plot Hi-C contact maps
HiC
hicrep
HiCcompare
3.5 years ago
changxu.fan
▴ 20
1
vote
7
replies
1.6k
views
problem recasting InteractionSet into a DGEList
diffHic
GenomicInteractions
edgeR
HiC
cooler
updated 3.7 years ago by
Aaron Lun
★ 28k • written 3.7 years ago by
Marco Blanchette
▴ 30
0
votes
1
reply
830
views
How to load counts from existing count matrices in diffHic package
diffHic
HiC
InteractionSet
updated 4.0 years ago by
Aaron Lun
★ 28k • written 4.0 years ago by
girardot
• 0
0
votes
1
reply
855
views
.cool to .txt cooler2bedpe does not work HiCompare
HiCompare
HiC
cool
updated 4.6 years ago by
Kevin Blighe
★ 3.9k • written 4.6 years ago by
c.chakraborty
• 0
0
votes
3
replies
1.5k
views
extracting scaffoldnames from HiC contact matrix
hic
updated 5.3 years ago by
bioparticles.melly
• 0 • written 5.3 years ago by
m.t.lorenc
• 0
0
votes
9
replies
1.5k
views
from denove contig assembly to chromosome bins
diffhic
gothic
hicup
hic-c
hic
updated 5.4 years ago by
Aaron Lun
★ 28k • written 5.4 years ago by
mictadlo
▴ 10
0
votes
1
reply
903
views
Error in scanBam(bam_fn) : could not find function "scanBam"
hic
diffhic
gothic
hicup
hic-c
5.4 years ago
mictadlo
▴ 10
1
vote
1
reply
1.3k
views
extract HiC contacts for a given BEDPE set of coordinates
hic
diffhic
chromatin
bedpe
updated 5.7 years ago by
Aaron Lun
★ 28k • written 5.7 years ago by
gryderart
• 0
2
votes
1
reply
1.2k
views
Inflating interactionSets into a contact matrix
diffhic
hic
interactionset
contactmatrix
inflate
updated 6.5 years ago by
Aaron Lun
★ 28k • written 6.5 years ago by
hwick1
▴ 20
0
votes
8
replies
1.6k
views
How to get specific fragment/read interactions from HiC (diffHiC) data?
diffhic
hic
updated 6.5 years ago by
Aaron Lun
★ 28k • written 6.5 years ago by
hwick1
▴ 20
2
votes
2
replies
1.4k
views
Extracting non-interacting hic reads to create a sam/bam file
diffhic
hicpro
hic
6.8 years ago • updated 6.7 years ago
sergio.espeso-gil
• 0
0
votes
3
replies
1.6k
views
GOTHiC hg19 error
GOTHiC
hic
8.6 years ago
Nathan Sheffield
▴ 10
4
votes
20
replies
2.4k
views
scaling loess curves
HiTC
gothic
diffhic
HiC
8.7 years ago • updated 8.6 years ago
Bogdan
▴ 670
17 results • Page
1 of 1
Recent ...
Replies
Comment: Deseq2 and Normalization of RNA sequencing data
by
ATpoint
★ 4.1k
There is no expectation of normality that is realistic in terms of expression level. Levels are widely different between genes, and counts …
Comment: Differences in differential analysis methods for RNA-Seq
by
ATpoint
★ 4.1k
MAGeCK is a command line tool that is easy to use. I recommend you use it because a) the logFCs from DESeq2 and MAGeCK will be very similar…
Comment: Get genomic coordinates of CpGs sites (chromosomes, genomic position)
by
Yveto
• 0
Thank for your response. It is Illumina 450 K. I use this code ```{r } library(IlluminaHumanMethylation450kanno.ilmn12.hg19) annotat…
Answer: More regions in union when increasing DBA$config$mergeOverlap
by
Rory Stark
★ 5.2k
I think the documentation is out of sync with the code. Positive values represent gaps between intervals and negative values represent how …
Comment: log2FoldChange value is way too different when compared with counts(dds)
by
Michael Love
41k
But just to be clear, this is not the same as regressing out batch from the VST (approx log transformed): ``` limma::removeBatchEffect(cou…
Votes
A: Error in DESeqDataSet : some values in assay are not integers
Bioconductor 3.19 is Released!
Bioconductor 3.19 is Released!
Answer: DEseq2 coefficient
SPIA plotP giving error
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