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Repository java_genomics_toolkit
Name: java_genomics_toolkit
Owner: timpalpant
Synopsis: Wig math (avg/log/Z-score/etc), NGS processing (ChIP-seq, MNase-seq, FAIRE-seq, DNase-seq), and visualization (heatmaps, clustering)
http://palpant.us/java-genomics-toolkit/
https://github.com/timpalpant/java-genomics-toolkit
Requires Java 7.
Content homepage: https://tim.palpant.us/java-genomics-toolkit/
Development repository: https://github.com/timpalpant/java-genomics-toolkit
Link to this repository: https://toolshed.g2.bx.psu.edu/view/timpalpant/java_genomics_toolkit/b43c420a6135
Clone this repository: hg clone https://toolshed.g2.bx.psu.edu/repos/timpalpant/java_genomics_toolkit
Type: unrestricted
Revision: 25:b43c420a6135
This revision can be installed: True
Times cloned / installed: 1919

Contents of this repository

Valid tools - click the name to preview the tool and use the pop-up menu to inspect all metadata
Name Description Version Minimum Galaxy Version
two (Big)Wig files 1.1.0 16.01
a (Big)Wig file 1.1.0 16.01
(Big)Wig files 1.1.0 16.01
that have been aligned 2.1.0 16.01
for a heatmap 1.0.0 16.01
a (Big)Wig file 1.1.0 16.01
from occupancy data 1.1.0 16.01
using matrix2png 1.0.0 16.01
in a DNA sequence 1.0.0 16.01
across a genomic interval 1.0.0 16.01
in an MNase experiment 1.1.0 16.01
of data in a Wiggle file 1.0.0 16.01
converter 1.1.0 16.01
of sequencing reads 2.0.0 16.01
from an interval file 1.0.0 16.01
of dyads 1.0.0 16.01
of data in a Wiggle file 2.0.0 16.01
over each locus 1.1.0 16.01
a (Big)Wig file 1.1.0 16.01
of a (Big)Wig file 1.1.0 16.01
of read lengths 1.0.0 16.01
in windows 2.0.0 16.01
by overlap 1.0.0 16.01
from Illumina to Sanger 1.0.0 16.01
using DynaPro 1.1.0 16.01
multiple (Big)Wig files 1.1.0 16.01
of a (Big)Wig file 1.1.0 16.01
of data in a (Big)Wig file 1.0.0 16.01
such as CNVs 1.1.0 16.01
a (Big)Wig file 1.2.0 16.01
from an aligned matrix 1.1.0 16.01
across a genomic interval 1.0.0 16.01
from sequencing reads 1.1.0 16.01
on any file 1.0.0 16.01
multiple (Big)Wig files 1.1.0 16.01
multiple (Big)Wig files 1.1.0 16.01
two (Big)Wig files 1.1.0 16.01
a (Big)Wig file 1.1.0 16.01
missing values in a (Big)Wig file 1.1.0 16.01
converter 1.1.0 16.01
in intervals 1.1.0 16.01
a (Big)Wig file 1.2.0 16.01
converter 1.1.0 16.01
a (Big)Wig file 1.2.0 16.01
converter 1.0.0 16.01
for a genomic interval 1.0.0 16.01
for a genome 2.0.0 16.01
an aligned matrix 1.0.0 16.01

Categories
Convert Formats - Tools for converting data formats
Graphics - Tools producing images
Statistics - Tools for generating statistics
Text Manipulation - Tools for manipulating data
Visualization - Tools for visualizing data