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Example usage — HiCExplorer 3.7.2 documentation
We have used the HiCExplorer successfully with bwa, bowtie2 and hisat2. However, it is important to: for either bowtie2`or `hisat2 use the –reorder parameter which tells bowtie2 or …
Hicexplorer.readthedocs.ioDA: 26 PA: 37 MOZ Rank: 63
hicConvertFormat — HiCExplorer 3.7.2 documentation - Read the …
HicConvertFormat. Conversion of Hi-C matrices of different file formats. We support the conversion of hic to cool format via hic2cool, and homer, HicPro, h5 and cool format to h5, …
Hicexplorer.readthedocs.ioDA: 26 PA: 46 MOZ Rank: 73
HiCExplorer | Read the Docs
HiCExplorer facilitates the creation of contact matrices, correction of contacts, TAD detection, A/B compartments, merging, reordering or chromosomes, conversion from different formats …
Readthedocs.orgDA: 15 PA: 22 MOZ Rank: 39
HiCExplorer Documentation - Read the Docs
HiCExplorer can be easily integrated into a localGalaxy. 8 Chapter 4. Contents: HiCExplorer Documentation, Release 2.0 Installation with Docker The HiCExplorer Galaxy instance is also …
Documentation-hicexplorer-test.readthedocs.ioDA: 45 PA: 30 MOZ Rank: 78
Installation — scHiCExplorer 7 documentation - Read the Docs
HiCExplorer 3.5. cooler 0.8.9. HiCMatrix 14. sparse-neighbors-search 0.6. Command line installation using conda ¶ The fastest way to obtain Python 3.6 together with numpy and scipy …
Schicexplorer.readthedocs.ioDA: 28 PA: 36 MOZ Rank: 68
hicCorrelate — HiCExplorer 2.0 documentation
HiCExplorer tools; Example usage; News and Developments; HiCExplorer. Docs » hicCorrelate; Edit on GitHub; hicCorrelate¶ Background; Description; Usage example. Heatmap; …
Documentation-hicexplorer-test.readthedocs.ioDA: 45 PA: 45 MOZ Rank: 95
Galaxy HiCExplorer - Galaxy Europe
A more advanced tutorial is hosted on readthedocs.io. It is designed for the shell based version of the HiCExplorer but can be easily adapted to Galaxy HiCExplorer. In this tutorial mouse …
Galaxyproject.euDA: 16 PA: 23 MOZ Rank: 45
scHiCExplorer
•HiCExplorer 3.5 •cooler 0.8.9 •HiCMatrix 14 •sparse-neighbors-search 0.6 6.1.2Command line installation using conda The fastest way to obtain Python 3.6together withnumpyandscipy is …
Schicexplorer.readthedocs.ioDA: 28 PA: 27 MOZ Rank: 62
News — scHiCExplorer 7 documentation
News¶ ** 4 Dezember 2020** Release of version 7: scHicClusterMinHash: Adding umap. adding option to color scatter plots with pre-classified information
Schicexplorer.readthedocs.ioDA: 28 PA: 28 MOZ Rank: 64
HiCExplorer · PyPI
With version 2.0, HiCExplorer is available for Python 2 and Python 3 and can be installed via: - Pip, Anaconda and GitHub for command line usage. - Toolshed and Docker …
Pypi.orgDA: 8 PA: 21 MOZ Rank: 38
scHiCExplorer
ScHiCExplorer,Release7 tool type inputfiles mainoutputfile(s) application scHicDemul-tiplex pre-pro-cess-ing 1 FASTQ file SRR to samplemappingfileBar-
Schicexplorer.readthedocs.ioDA: 28 PA: 27 MOZ Rank: 65
High-resolution TADs reveal DNA sequences underlying genome …
Here we use our software, HiCExplorer (hicexplorer.readthedocs.io) to annotate >2800 high-resolution (570 bp) TAD boundaries in Drosophila melanogaster. We identify eight …
Nature.comDA: 14 PA: 28 MOZ Rank: 53
hic_matrix — pyGenomeTracks 3.7 documentation - Read the Docs
This is useful to plot multiple hic-matrices on the same scale # scale_factor = 1 # You can choose to keep the matrix as not rasterized # (only used if you use pdf or svg output format) …
Pygenometracks.readthedocs.ioDA: 29 PA: 41 MOZ Rank: 82
Very low percentage of pair used · Issue #361 · …
I am also struggling to understand why most experiments I QC are returning very low "pairs used" (<20%), I pipeline hicExplorer with snakemake so it's fairly reproducible. …
Github.comDA: 10 PA: 33 MOZ Rank: 56
hic_matrix_square — pyGenomeTracks 3.7 documentation - Read …
Optional:¶ title: Put here a title which will apprear on the right.. height: 0.5 (default) or float above 0.. overlay_previous: no (default) or yes or share-y.. orientation: by default this option is not set …
Pygenometracks.readthedocs.ioDA: 29 PA: 48 MOZ Rank: 91
Ltrpred — RCAC Biocontainers v1.0 documentation
Warning. Using #!/bin/sh-l as shebang in the slurm job script will cause the failure of some biocontainer modules. Please use #!/bin/bash instead.
Biocontainer-doc.readthedocs.ioDA: 31 PA: 38 MOZ Rank: 84
Adding new tracks — pyGenomeTracks 3.7 documentation - Read …
The output of HiCExplorer hicFindTADs produces a file whose data format is similar to a bedgraph but with more value columns. We call this a bedgraph matrix. The following track …
Pygenometracks.readthedocs.ioDA: 29 PA: 38 MOZ Rank: 83
hic_matrix — pyGenomeTracks 3.7 documentation
Optional:¶ title: Put here a title which will apprear on the right.. height: If you do not set it, the height will be adjusted so that each bin is a square, else you can choose any float above 0.. …
Pygenometracks.readthedocs.ioDA: 29 PA: 38 MOZ Rank: 84
Clair3 — RCAC Biocontainers v1.0 documentation
Clair3 Introduction . Clair3 is a germline small variant caller for long-reads. Clair3 makes the best of two major method categories: pileup calling handles most variant candidates with speed, …
Biocontainer-doc.readthedocs.ioDA: 31 PA: 36 MOZ Rank: 85
deprecate liberman format as import/export · Issue #257 · …
Extending on the conversation about import/export of matrices, I think it's valid to support multiple input formats and keep only one output format. We should also deprecate liberman format …
Github.comDA: 10 PA: 33 MOZ Rank: 62
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| Site | Provider | Expiration Date |
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| howthestockmarketworks.com | above.com | 117 Days |
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