A small cross-platform browser for prokaryotic HiC maps.

ProHiC provides handy GUI for visualizing and browsing HiC contact maps of small circular genomes and related tracks. It contains unique features, such as genome rolling, instant observed/expected map computing, extremely convenient colorscale adjusting.

ProHiC is tested on Windows, Linux, MacOS. Portable version for Windows is also availabe.

To install ProHiC, you should have python higher then 3.8 and pip installed on your computer. If you don't have one of them, see below. When all conditions are met, browser can be installed from github with pip.

pip install https://github.com/a17sol/ProHiC/archive/master.zip

See Installation details for details on how to install the program on your operating system, additional steps may be required.

After installation it is possible to create a desktop shortcut with simple command:

prohic shortcut

On some systems (e.g. Ubuntu) you should manually allow launching in the right-button menu of the shortcut.

1. Download installer (e.g. here)
2. Run inastaller. Select options:
   • First screen: Add Python3.9 to PATH, Customize installation
   • Second screen: Only pip and py launcher
   • Third screen: default

You have three options:

1. Use a portable version
2. Uninstall existing version and install 3.9 as described above. Make sure that this does not cause incompatibilities with other applications.
3. Use conda environment.

1. Download installer (here)
2. Run it as administrator

Run cmd.exe and type

pip install https://github.com/a17sol/ProHiC/archive/master.zip

On Mac with Apple processor you always need to use conda environment with pip installed inside, as these pocessors does not support some of the standard packages.

1. Download installer (e.g. here)
2. Run inastaller.

You have two options:

1. Uninstall existing version and install 3.9 as described above. Make sure that this does not cause incompatibilities with other applications.
2. Use conda environment. It is safe, but a bit more difficult.

pip always come with python, but in case you need, you can use

python3 -m ensurepip

Run Terminal and type

sudo pip install https://github.com/a17sol/ProHiC/archive/master.zip

In most cases sudo is not really necessary, but is recommended.

Note that all modern versions of Ubuntu have one version of python installed. If your preinstalled version is inappropriate, see below. If you really need to install it, use the terminal command

sudo apt install python3.9

You have two options:

1. Uninstall existing version and install 3.9 as described above. Make sure that this does not cause incompatibilities with other applications.
2. Use conda environment. It is safe, but a bit more difficult.

Use terminal command

sudo apt install python3-pip

Run Terminal and type

sudo apt-get install libxcb-xinerama0
sudo pip install https://github.com/a17sol/ProHiC/archive/master.zip

To download the portable version for Windows, click here.

Relevant repository is ProHiC_portable

To uninstall browser just use

pip uninstall prohic

Note that desktop shortcut should be removed manually.

You can start browser with command

prohic

or by clicking desktop shortcut.

All functioanality is available though GUI, and main functions - though key bindings.

Note the functionality, that could be not obvious enough:

• Click on gene/region shows its name and info
• Click on Y-axis of graph track toggles logarithmic mode
• Right-click on map provides "View all" option and allows to export view
• Right-click menu of graph-tracks allows to set Y-autorange to visible data only
• Right-click on colorscale resets it
• Disabling log colorscale may be useful when browsing observed/expected map

Acceptable formats:

• HiC-map - .cool, .mcool, .np (numpy savetxt files, useful option for quick testing of map processing algorithms etc.)
• Gene/region track - .bed, .gff, .gff2, .gff3
• Graph track - .bedgraph