Showing : hic • reset
0
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92
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Question about RE-agnostic mode for intact Hi-C and Micro-C normalization(HiCDCPlus)
HiC HiCDCPlus
written 8 days ago by • 0
0
votes
0
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562
views
hichip fragments extraction chip seq
ChIPSeqData interact GenomicRanges HiC
16 months ago user_bioinfo • 0
0
votes
2
replies
796
views
Java error while running HiCDC overview code
JuicerTools HiC HiCDCPlus Java Juicer
written 2.0 years ago by • 0
0
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0
replies
1.4k
views
Job: Bioinformatics Research Scientist- Epigenetics Group
HiC Epigenetics HiCHIP ChIPSeq
3.5 years ago xubeisi • 0
0
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0
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1.5k
views
How to prepare HiCUP BAM output as input for HOMER?
HOMER HiCUP BAM HiC
4.1 years ago Ankit ▴ 20
0
votes
3
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1.3k
views
HiCDCPlus / HiC-DC+ is not found
HiCDCPlus HiC-DC+ HiCcompare HiC
updated 3.6 years ago by • 0 • written 5.1 years ago by • 0
0
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0
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927
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 ★ 29k • written 5.3 years ago by ▴ 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 ★ 29k • written 5.6 years ago by • 0
0
votes
1
reply
1.4k
views
.cool to .txt cooler2bedpe does not work HiCompare
HiCompare HiC cool
updated 6.2 years ago by ★ 4.0k • written 6.2 years ago by • 0
0
votes
3
replies
2.1k
views
extracting scaffoldnames from HiC contact matrix
hic
updated 6.9 years ago by • 0 • written 6.9 years ago by • 0
0
votes
9
replies
2.4k
views
from denove contig assembly to chromosome bins
diffhic gothic hicup hic-c hic
updated 7.0 years ago by ★ 29k • written 7.0 years ago by ▴ 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
2.1k
views
extract HiC contacts for a given BEDPE set of coordinates
hic diffhic chromatin bedpe
updated 7.3 years ago by ★ 29k • written 7.3 years ago by • 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 ★ 29k • written 8.1 years ago by ▴ 20
0
votes
8
replies
2.4k
views
How to get specific fragment/read interactions from HiC (diffHiC) data?
diffhic hic
updated 8.2 years ago by ★ 29k • written 8.2 years ago by ▴ 20
2
votes
2
replies
1.9k
views
Extracting non-interacting hic reads to create a sam/bam file
diffhic hicpro hic
8.4 years ago sergio.espeso-gil • 0
0
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3
replies
2.1k
views
GOTHiC hg19 error
GOTHiC hic
10.3 years ago • updated 10.2 years ago Nathan Sheffield ▴ 10
4
votes
20
replies
3.6k
views
scaling loess curves
HiTC gothic diffhic HiC
10.3 years ago Bogdan ▴ 670
19 results • Page 1 of 1
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Answer: NUPOP usage by shepherl 4.2k
You should read the documentation in the package especially the package vignette https://bioconductor.org/packages/release/bioc/html/NuPoP.…
Comment: How can I correctly use phyloseq with Docker? by fnfgame • 0
In a rocker image, this error usually means the Bioconductor install happened as root but the runtime library paths used by the shiny user …
Comment: DECIPHER DesignProbes unable to design FISH-probes by Erik Wright ▴ 150
Are the sequences aligned (i.e., the same width) before running `TileSeqs()`?
Comment: BiocParallel (and DESeq2) - wrong args for environment subassignment by Michael Love 43k
BTW, I tested with no issue on MacOS ARM on our previous github issue.
Answer: DESeq(dds, parallel=TRUE) wrong args for environment subassignment by Michael Love 43k
The DESeq2 error makes sense, as we've talked about, given that the simple `bplapply` isn't working in your setup. Maybe give the traceb…
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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