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hic
•
reset
0
votes
0
replies
308
views
hichip fragments extraction chip seq
ChIPSeqData
interact
GenomicRanges
HiC
6 months ago
user_bioinfo
• 0
0
votes
2
replies
554
views
Java error while running HiCDC overview code
JuicerTools
HiC
HiCDCPlus
Java
Juicer
written 14 months ago by
IsMM
• 0
0
votes
0
replies
1.1k
views
Job:
Bioinformatics Research Scientist- Epigenetics Group
HiC
Epigenetics
HiCHIP
ChIPSeq
2.7 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
3.2 years ago
Ankit
▴ 20
0
votes
3
replies
1.1k
views
HiCDCPlus / HiC-DC+ is not found
HiCDCPlus
HiC-DC+
HiCcompare
HiC
updated 2.8 years ago by
merve.sahn
• 0 • written 4.3 years ago by
mtS
• 0
0
votes
0
replies
732
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 4.5 years ago by
Aaron Lun
★ 28k • written 4.5 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 5.4 years ago by
Kevin Blighe
★ 4.0k • written 5.4 years ago by
c.chakraborty
• 0
0
votes
3
replies
1.8k
views
extracting scaffoldnames from HiC contact matrix
hic
updated 6.1 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 6.2 years ago by
Aaron Lun
★ 28k • written 6.2 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
mictadlo
▴ 10
1
vote
1
reply
1.7k
views
extract HiC contacts for a given BEDPE set of coordinates
hic
diffhic
chromatin
bedpe
updated 6.5 years ago by
Aaron Lun
★ 28k • written 6.5 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
2.0k
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
1.7k
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
3.0k
views
scaling loess curves
HiTC
gothic
diffhic
HiC
9.5 years ago • updated 9.4 years ago
Bogdan
▴ 670
18 results • Page
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Answer: SingleR with multiple single cell references
by
Aaron Lun
★ 28k
> Is it necessary to piece together the individual steps manually (e.g. aggregateReference, trainSingleR, classifySingleR, combineRecompute…
Answer: Automatically install dependencies
by
ATpoint
★ 4.7k
The BiocManager, which is sort of an extended wrapper around `install.packages`, installs all R dependencies. If you see errors then this i…
Answer: To count or not to count multi-overlapping reads?
by
Gordon Smyth
52k
> How does it handle reads that map to a gene that is located in a region that also has another gene but on the alternate strand? Overlapp…
Comment: Weird p-values using DESeq2?
by
ATpoint
★ 4.7k
This does not look like normalized counts but raw counts. Consider using `counts(dds, normalized = TRUE)` or the output of `normTransform()…
Answer: Weird p-values using DESeq2?
by
Wolfgang Huber
★ 13k
Dear Ingrid, thank you for asking. Can you provide the input count matrix (you can "pseudonymize" the biological conditions and the gene n…
Votes
A: Fraction count for multi mapping reads; how to generate input file for Deseq2 fo
Comment: Weird p-values using DESeq2?
Comment: Overcoming confounding in batch effect correction
Answer: Store Matrix in DataFrame Cell
Answer: enrichGOgradient color change
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