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Showing top results for tag: Hi-C • reset
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69
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pipeline/software/script to connect (whatshap) VCF phase blocks with Hi-C reads
whatshap phasing pipeline Hi-C
4 weeks ago by mvk ▴ 10
0
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5
replies
394
views
How to adjust p value after Wilcoxon rank sum test?
p-value TADs statistics Hi-C
updated 6 weeks ago by 49k • written 6 weeks ago by • 0
1
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0
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133
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How to convert a HG19 Hi-C hic file to HG38?
Hi-C hic
11 weeks ago by Ian 5.7k
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0
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130
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Hi-C merged files
Hi-C .hic
3 months ago by Oleczkaff • 0
0
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0
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95
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Is there a way to subsample Hi-C at Hi-C matrix .cool file?
Hi-C loops
3 months ago by sckinta ▴ 660
0
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1
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377
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How to plot scaling curves for Hi-C data?
Hi-C
updated 4 months ago by • 0 • written 10 months ago by • 0
6
votes
3
replies
499
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recent Hi-C databases
hi-C 4C 3C
updated 5 months ago by ▴ 50 • written 8 months ago by ★ 1.1k
3
votes
1
reply
244
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HI-C analysis in the cloud environment
HI-C
updated 5 months ago by ▴ 50 • written 6 months ago by ★ 1.1k
0
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3
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851
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ICE normalization using JuicerTools
Hi-C genome 3c juicer cooler
updated 5 months ago by ▴ 50 • written 8 months ago by • 0
2
votes
3
replies
2.1k
views
Hi-C contact probability
hi-c
updated 5 months ago by • 0 • written 4.5 years ago by ▴ 440
0
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0
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153
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Plot only the genome-wide trans contacts in a Hi-C matrix (no cis contacts)
juicer Hi-C inter-chromosomal cooler trans
5 months ago by kalavattam ▴ 50
0
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1
reply
241
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Bioinformatics definition of TAD boundary
hiTADs Hi-C TAD
updated 4 months ago by ▴ 50 • written 5 months ago by ▴ 660
3
votes
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 2.7 years ago by 100k • written 2.7 years ago by 138k
0
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2
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317
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How to validate existing networks with co-expression
RNA-Seq Hi-C gene enhancer
updated 10 months ago by ▴ 190 • written 10 months ago by ▴ 10
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0
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236
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Looking for a fast way to visualize the same region of many Hi-C datasets together
Hi-C juicer juicebox
11 months ago by changxu.fan ▴ 50
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1
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1.2k
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HOMER Hi-C with more than one enzyme
Hi-C HOMER
updated 11 months ago by • 0 • written 3.7 years ago by ★ 1.6k
0
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0
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289
views
How to count the paired end reads number in given regions
paired-end bam Hi-C HiC-Pro
12 months ago by ben.kunfang ▴ 30
2
votes
2
replies
303
views
How to deal with Hi-C replicates from different patients' tissue sample?
Hi-C patient replicates
updated 13 months ago by ★ 3.4k • written 13 months ago by ▴ 30
0
votes
0
replies
400
views
Explaining myJuicer.sh different steps
hi-c juicer
13 months ago by Rox ★ 1.3k
1
vote
1
reply
373
views
Help required to understand Hi-C data and it's Usage
Hi-C Forum
updated 14 months ago by ▴ 160 • written 14 months ago by ▴ 360
0
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0
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509
views
News: ONLINE COURSE. Eukaryotic genome assembly USING Pacbio and Hi-C
assembly pacbio long-reads HI-C News
15 months ago by carlopecoraro2 ★ 2.0k
0
votes
0
replies
404
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 16 months ago by 20 • written 18 months ago by • 0
0
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0
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255
views
Genotype calling from Hi-C data
Hi-C genotyping
17 months ago by euge.eugenio • 0
2
votes
0
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531
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How to query a hic file for whether two regions contact
hi-c juicer
updated 18 months ago by 20 • written 19 months ago by ▴ 990
0
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0
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343
views
Hi-c Phase block Viewer
Hi-C 10x phase block SNP Haploview
21 months ago by tothepoint ▴ 600
0
votes
0
replies
492
views
How to address location of temporary file issue when converting Homer tag directories to hi-c files?
homer juicer hi-c juicer_tools
21 months ago by J.J. on Biostars • 0
1
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0
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668
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
21 months ago by ricardo3889 ▴ 40
2
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0
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2.3k
views
Job: Postdoctoral position, Bioinformatics Division, Walter and Eliza Hall Institute of Medical Research, Australia
Hi-C Job Australia
23 months ago by Gordon Smyth ★ 3.4k
0
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0
replies
720
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Job: Post-doc position in 3D chromatin organization
ChIP-Seq Hi-C super-resolution microscopy Job
24 months ago by alessio.zippo • 0
0
votes
0
replies
346
views
how to calculate the contact frequency between promoter and enhancer
Hi-C
2.0 years ago by BenHu • 0
0
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0
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529
views
Getting Hi-C contact matrix from single cell experiment
hi-c single-cell
updated 2.2 years ago by 20 • written 2.3 years ago by • 0
0
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0
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512
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Error processing Hi-data using HiCUP
Hi-C HiCUP Forum NGS
updated 2.3 years ago by 46k • written 2.3 years ago by ▴ 40
0
votes
0
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414
views
Segment the genome in an unbiased way
genome sequencing Hi-C
2.4 years ago by ste.lu ▴ 80
1
vote
1
reply
818
views
Your favourite workflow for Hi-C data analysis (Plant Genome)
Hi-C
updated 2.4 years ago by 20 • written 2.5 years ago by ★ 2.7k
0
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0
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348
views
Help extracting Hi-C contacts from binaries provided in Bonev et al. 2017
R genome Hi-C
2.5 years ago by elyk_bear • 0
2
votes
2
replies
490
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What all We can do with Hi-C data
Hi-C New Ideas
2.6 years ago by biofreek • 0
1
vote
3
replies
868
views
Analysis pipeline for 3e Hi-C
Hi-C 3e Hi-C multi-enzyme digestion
2.7 years ago by ancient_learner ▴ 650
5
votes
9
replies
1.3k
views
Hi-C data alignment with star
star hi-c
updated 2.7 years ago by ▴ 340 • written 2.7 years ago by ★ 2.7k
2
votes
2
replies
1.2k
views
Paired-end flag for singleton
Hi-C sequencing Paired-end sequencing samtools
updated 2.9 years ago by ▴ 570 • written 2.9 years ago by • 0
2
votes
3
replies
2.3k
views
How to visualize Hi-C bed file format?
genome Hi-C
3.1 years ago by mkh ▴ 50
8
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4
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2.4k
views
Figuring out HiC restriction enzyme
Hi-C HiC scaffolding
updated 26 days ago by • 0 • written 3.5 years ago by ▴ 110
0
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0
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671
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News: Course "Epigenetics: on the top of genetics", Udine, Italy, 4-7 September 2018
ChIP-Seq hi-c smallRNA NGS BS-seq News
3.1 years ago by Fabio Marroni ★ 2.8k
1
vote
0
replies
1.6k
views
Job: Bioinformatics Postdoc in Aging, Harvard Medical School
RNA-Seq ChIP-Seq Job Hi-C aging
updated 3.1 years ago by 34k • written 3.1 years ago by ▴ 10
1
vote
2
replies
1.1k
views
visualize Hi-C .cool file in R
Hi-C
3.2 years ago by ta_awwad ▴ 310
0
votes
0
replies
620
views
Missing Interaction Frequencies
Hi-C HiC
3.3 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 3.5 years ago by 16k • written 3.6 years ago by ▴ 20
0
votes
0
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902
views
How to annotate peaks inside TADs and annotated with Gene expression?
ChIP-Seq HI-C RNA-Seq
3.6 years ago by carlosalfonsogonzalez6 ▴ 10
1
vote
1
reply
828
views
How to continue processing Hi-C reads
chromatin capture hi-C chromatin conformation
3.8 years ago by Hushus ▴ 20
3
votes
11
replies
1.0k
views
What do the columns in this Hi-C file relate to?
Hi-C Chromatin Capture
3.8 years ago by Hushus ▴ 20
0
votes
0
replies
1.4k
views
Job: Postdoctoral Researcher Systems Biology/Personalized Medicine, Perth, Australia
bioinformatics hi-c wgs Job
3.9 years ago by Philipp Bayer 7.3k
50 results • Page 1 of 1
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Which files from PacBio output files to use in downstream analysis in R
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Recent Replies
Comment: Error message running GeMoMa by Dardo • 0
can you solve this problem? this is my problem too
Comment: How to download BLAST+ on Centos (6) by Nelo • 0
okie Tnkq
Comment: Need help to remove NA values from data frame by ponganta ▴ 490
Agreed, especially regarding `dplyr::rename()`. I didn't think about that. Regarding these two functions, there are oftentimes namespace …
Comment: blast culling_limit option behavior by joe.westley • 0
Hi GenoMax, sorry for the late response. Yes I am looking to only keep one hit. I am not sure I follow the idea that all the reported hit…
Comment: Splice aware vs splice unaware aligners? by GenoMax 107k
Spliced transcripts will bring together ends of exons that may be much farther apart in the genome. A short illumina read can now cover tha…
Answer: Splice aware vs splice unaware aligners? by jaqx008 ▴ 90
Splice aware aligners like tophat, STAR provide bam out put with spliced junction information (specific locations where introns are removed…
Answer: Splice aware vs splice unaware aligners? by lieven.sterck 12k
splice aware aligners take into account to 'split' the alignment only when it is compliant to the correct use of splice sites (donor & acce…
Comment: How to download BLAST+ on Centos (6) by Michael Dondrup 49k
This is a problem with Centos 6, it is so old that most 'modern' software (including software installed via conda) does not run because it…
Comment: How to download BLAST+ on Centos by Nelo • 0
I followed your step mentioned above and BLAST is installed. But now I trying to create a local database using multiple fasta files using c…
Comment: New in DiffBind: dba.plotProfile() - Peak profiles and profile heatmaps by Rory Stark ★ 1.2k
Hmmn, I'm not sure where that is coming from. In the released version of `dba.plotProfile()`, there shouldn't be any dependencies on the re…
Answer: How To Interpret PLINK's plink.lasso File by 1311703846 • 0
i think the "effect" is something like beta in regression model, it estimate the effect A1 has to impact the phenotype value, like when pe…
Comment: How to download BLAST+ on Centos by GenoMax 107k
If you followed the steps I had outlined above no installation should be needed. Is that copy of blast not working? You should be able to s…
Comment: How to download BLAST+ on Centos by Nelo • 0
yes you're right. While updating the version 2.14 glibc on my centos 6, its not going further after configuration step as it is seeking per…
Answer: Issues with R studio installation by colindaven ★ 3.1k
I don't know what these packages are called on OpenSuse - you'll have to install them, and the one you mention above, using the zypper tool…
Comment: PRS in UK Biobank - no covariate file and no phenotype file by agamemnon • 0
Is there any difference between data-field ```41202``` and ```41270```?
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