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Showing top results for tag: Hi-C • reset
0
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0
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69
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How to convert a HG19 Hi-C hic file to HG38?
Hi-C hic
17 days ago by Ian 5.7k
0
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0
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81
views
Hi-C merged files
Hi-C .hic
6 weeks ago by Oleczkaff • 0
0
votes
0
replies
62
views
Is there a way to subsample Hi-C at Hi-C matrix .cool file?
Hi-C loops
7 weeks ago by sckinta ▴ 660
0
votes
1
reply
308
views
How to plot scaling curves for Hi-C data?
Hi-C
updated 9 weeks ago by • 0 • written 8 months ago by • 0
6
votes
3
replies
430
views
recent Hi-C databases
hi-C 4C 3C
updated 3 months ago by ▴ 50 • written 6 months ago by ★ 1.1k
3
votes
1
reply
210
views
HI-C analysis in the cloud environment
HI-C
updated 3 months ago by ▴ 50 • written 4 months ago by ★ 1.1k
0
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3
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632
views
ICE normalization using JuicerTools
Hi-C genome 3c juicer cooler
updated 3 months ago by ▴ 50 • written 6 months ago by • 0
2
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3
replies
2.0k
views
Hi-C contact probability
hi-c
updated 3 months ago by • 0 • written 4.3 years ago by ▴ 440
0
votes
0
replies
123
views
Plot only the genome-wide trans contacts in a Hi-C matrix (no cis contacts)
juicer Hi-C inter-chromosomal cooler trans
3 months ago by kalavattam ▴ 50
0
votes
1
reply
193
views
Bioinformatics definition of TAD boundary
hiTADs Hi-C TAD
updated 10 weeks ago by ▴ 50 • written 3 months ago by ▴ 660
3
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5
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1.5k
views
Hi-C: getting intervals from "A Compendium of Chromatin Contact Maps Reveal Spatially Active Regions in the Human Genome"
Hi-C intervals chromosome interaction tad
updated 2.5 years ago by 99k • written 2.5 years ago by 137k
0
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2
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257
views
How to validate existing networks with co-expression
RNA-Seq Hi-C gene enhancer
updated 8 months ago by ▴ 190 • written 8 months ago by ▴ 10
0
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0
replies
203
views
Looking for a fast way to visualize the same region of many Hi-C datasets together
Hi-C juicer juicebox
9 months ago by changxu.fan ▴ 50
0
votes
1
reply
1.1k
views
HOMER Hi-C with more than one enzyme
Hi-C HOMER
updated 9 months ago by • 0 • written 3.5 years ago by ★ 1.6k
0
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0
replies
259
views
How to count the paired end reads number in given regions
paired-end bam Hi-C HiC-Pro
10 months ago by ben.kunfang ▴ 30
2
votes
2
replies
265
views
How to deal with Hi-C replicates from different patients' tissue sample?
Hi-C patient replicates
updated 11 months ago by ★ 2.8k • written 11 months ago by ▴ 30
0
votes
0
replies
309
views
Explaining myJuicer.sh different steps
hi-c juicer
11 months ago by Rox ★ 1.3k
1
vote
1
reply
344
views
Help required to understand Hi-C data and it's Usage
Hi-C Forum
updated 12 months ago by ▴ 130 • written 12 months ago by ▴ 330
0
votes
0
replies
431
views
News: ONLINE COURSE. Eukaryotic genome assembly USING Pacbio and Hi-C
assembly pacbio long-reads HI-C News
13 months ago by carlopecoraro2 ★ 2.0k
0
votes
0
replies
360
views
Any tool/database that can map SNPs to genes based on Hi-C & eQTL data, not by closest genes?
MAGMA Chromatin capture Hi-C eQTL
updated 14 months ago by 20 • written 16 months ago by • 0
0
votes
0
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227
views
Genotype calling from Hi-C data
Hi-C genotyping
14 months ago by euge.eugenio • 0
2
votes
0
replies
463
views
How to query a hic file for whether two regions contact
hi-c juicer
updated 16 months ago by 20 • written 17 months ago by ▴ 990
0
votes
0
replies
308
views
Hi-c Phase block Viewer
Hi-C 10x phase block SNP Haploview
18 months ago by devarora ▴ 520
0
votes
0
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439
views
How to address location of temporary file issue when converting Homer tag directories to hi-c files?
homer juicer hi-c juicer_tools
19 months ago by J.J. on Biostars • 0
1
vote
0
replies
599
views
obtaining mean contact/interaction frequency of a given 2D genomic region (loops from from bedpe file) from a hic matrix
HiC Hi-C Bedpe matrix R
19 months ago by ricardo3889 ▴ 40
1
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0
replies
2.2k
views
Job: Postdoctoral position, Bioinformatics Division, Walter and Eliza Hall Institute of Medical Research, Australia
Hi-C Job Australia
20 months ago by Gordon Smyth ★ 2.8k
0
votes
0
replies
685
views
Job: Post-doc position in 3D chromatin organization
ChIP-Seq Hi-C super-resolution microscopy Job
22 months ago by alessio.zippo • 0
0
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0
replies
320
views
how to calculate the contact frequency between promoter and enhancer
Hi-C
22 months ago by BenHu • 0
0
votes
0
replies
497
views
Getting Hi-C contact matrix from single cell experiment
hi-c single-cell
updated 2.0 years ago by 20 • written 2.1 years ago by • 0
0
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0
replies
468
views
Error processing Hi-data using HiCUP
Hi-C HiCUP Forum NGS
updated 2.2 years ago by 45k • written 2.2 years ago by ▴ 40
0
votes
0
replies
388
views
Segment the genome in an unbiased way
genome sequencing Hi-C
2.2 years ago by ste.lu ▴ 80
1
vote
1
reply
764
views
Your favourite workflow for Hi-C data analysis (Plant Genome)
Hi-C
updated 2.2 years ago by 20 • written 2.3 years ago by ★ 2.7k
0
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0
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320
views
Help extracting Hi-C contacts from binaries provided in Bonev et al. 2017
R genome Hi-C
2.3 years ago by elyk_bear • 0
2
votes
2
replies
457
views
What all We can do with Hi-C data
Hi-C New Ideas
2.4 years ago by biofreek • 0
1
vote
3
replies
800
views
Analysis pipeline for 3e Hi-C
Hi-C 3e Hi-C multi-enzyme digestion
2.5 years ago by ancient_learner ▴ 640
5
votes
9
replies
1.2k
views
Hi-C data alignment with star
star hi-c
updated 2.5 years ago by ▴ 340 • written 2.5 years ago by ★ 2.7k
2
votes
2
replies
1.1k
views
Paired-end flag for singleton
Hi-C sequencing Paired-end sequencing samtools
updated 2.7 years ago by ▴ 570 • written 2.7 years ago by • 0
2
votes
3
replies
2.2k
views
How to visualize Hi-C bed file format?
genome Hi-C
2.9 years ago by mkh ▴ 40
6
votes
4
replies
2.2k
views
Figuring out HiC restriction enzyme
Hi-C HiC scaffolding
updated 2.9 years ago by ▴ 110 • written 3.3 years ago by ▴ 100
0
votes
0
replies
646
views
News: Course "Epigenetics: on the top of genetics", Udine, Italy, 4-7 September 2018
ChIP-Seq hi-c smallRNA NGS BS-seq News
3.0 years ago by Fabio Marroni ★ 2.7k
1
vote
0
replies
1.6k
views
Job: Bioinformatics Postdoc in Aging, Harvard Medical School
RNA-Seq ChIP-Seq Job Hi-C aging
updated 3.0 years ago by 34k • written 3.0 years ago by ▴ 10
1
vote
2
replies
1.0k
views
visualize Hi-C .cool file in R
Hi-C
3.0 years ago by ta_awwad ▴ 310
0
votes
0
replies
588
views
Missing Interaction Frequencies
Hi-C HiC
3.1 years ago by Dogancan ▴ 30
3
votes
1
reply
1.3k
views
long-range technologies for genome scaffolding
scaffolding Nanopore Hi-C optical maps 10X
updated 3.3 years ago by 16k • written 3.5 years ago by ▴ 20
0
votes
0
replies
856
views
How to annotate peaks inside TADs and annotated with Gene expression?
ChIP-Seq HI-C RNA-Seq
3.4 years ago by carlosalfonsogonzalez6 ▴ 10
1
vote
1
reply
793
views
How to continue processing Hi-C reads
chromatin capture hi-C chromatin conformation
3.6 years ago by Hushus ▴ 20
3
votes
11
replies
992
views
What do the columns in this Hi-C file relate to?
Hi-C Chromatin Capture
3.7 years ago by Hushus ▴ 20
0
votes
0
replies
1.3k
views
Job: Postdoctoral Researcher Systems Biology/Personalized Medicine, Perth, Australia
bioinformatics hi-c wgs Job
3.7 years ago by Philipp Bayer 7.1k
0
votes
2
replies
902
views
Hi-C, inferring contacts from normalized matrixes
chromatine Hi-C
3.7 years ago by R.Blues ▴ 130
0
votes
0
replies
750
views
Hi-C, compartments, issue with some chromosomes
hi-c compartments
3.8 years ago by int11ap1 ▴ 440
50 results • Page 1 of 1
Recent Votes
Answer: What's the biggest thing you dislike about bioinformatics?
Comment: opening downloaded files from STRING protein network without R
Comment: What's the biggest thing you dislike about bioinformatics?
Gene Set Enrichment Analysis
Comment: Removing genes of Seurat object during integration pipeline
How to generate a .sam/.bam file of a particular chromosome or even a particular region?
How To Split A Bam File By Chromosome
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Recent Replies
Comment: inquiry related to snpsift by rheab1230 • 0
the command: java -jar SnpSift.jar annotate dbSnp144.vcf variants.vcf > variants_annotated.vcf I am getting no error. the input file …
Comment: Displaying points which fall outside of the plot window in EnhancedVolcano by os306 ▴ 10
Hi there, just to follow up on this, I used your package to generate my volcano plots and got exactly what I was looking for. I now wish to…
Comment: inquiry related to snpsift by Kevin Blighe 75k
Hi, please show: 1. the command(s) that you are using 2. a sample of your input data 3. a sample of your output data 4. any status, wa…
Comment: opening downloaded files from STRING protein network without R by fionajcunningham • 0
thanks GenoMax I will try this sorry for delay in reply!! Fiona
Comment: What's the biggest thing you dislike about bioinformatics? by WouterDeCoster 45k
The alternative, constant off-by-one errors, aren't my idea of fun either :-)
Comment: Removing genes of Seurat object during integration pipeline by Stevens • 0
Yeah, you can filter min_cells in Seurat with SCtransform. That would probably change the gene numbers in the SCT assay of the object. I u…
Comment: Removing genes of Seurat object during integration pipeline by ATpoint 52k
Doesn't sctransform has a `min_cells` parameter that you could use here? It will only consider genes detected in at least `min_cells` cells…
Comment: Removing genes of Seurat object during integration pipeline by Stevens • 0
I was thinking of making it an arbitrary cut off of 10 cells, Seurat's documentation uses 3 for reading in a single sample. I believe that …
Answer: How To Split A Bam File By Chromosome by etiennedanis • 0
With samtools v1.11, ```samtools view -b in.bam chr1 > out.bam``` did not work for me. But ```samtools view -b in.bam 1 > out.bam``` wo…
Comment: Removing genes of Seurat object during integration pipeline by ATpoint 52k
What is a "few" cells? So how many? You would need to manually calculate the fraction of cells expressing a certain gene. Not sure in which…
Comment: I want to make a graph for conserved regions by sa.youssef • 0
Thanks so much, it is a great suggestion. may I ask you if you know a way to visualize the results of these data in my report? as we are wo…
Comment: Minfi - estimateCellCounts by Papyrus ★ 1.1k
I understand that you have whole blood samples and that's why you expect them to have more granulocytes? You could also try the [ENmix][1] …
Comment: error related to SnpSift by rheab1230 • 0
I am able to do this. I downloaded the .tar file instead of using conda
Comment: What's the biggest thing you dislike about bioinformatics? by Ram 34k
I'll join you. I am not a fan of python either.
Comment: SNP filtering by Ram 34k
Please pay close attention to [the command I wrote initially][1]. The correct command is `tabix -p vcf GEUVADIS.chr1.genotype.vcf.gz` The `…
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