The software is released under a the Apache License, Version 2.0 (the "License"); You may obtain a copy of the License at http://www.apache.org/licenses/LICENSE-2.0. Unless required by applicable law or agreed to in writing, software distributed under the License is distributed on an "AS IS" BASIS, WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. See the License for the specific language governing permissions and limitations under the License.

The web site is developped in PHP and the data is stored with a Mysql database. We are also using jQuery and Font Awesome in the web pages.

The analyses rely on predefined, easily customizable modular scripts to invoke the most common analysis steps:

• FastX-toolkits and FastQC tools are used to filter reads and control the quality of all raw data.
• BWA, TopHat and Bismark are the options for the reads alignment of ChIP-seq, RNA-seq and DNA-methylation reads, respectively.
• MACS is used for peak calling and saturation analysis.
• The Bioconductor diffBind is used for differential peak calling of ChIP-seq data.
• Cufflinks and Cuffdiff, or alternatively Bioconductor tools including edgeR and DESeq are available for the absolute and differential quantification of expression.
• The methylPipe R library is used for the analysis of DNA methylation data.
• The INSPEcT R library is used for the analysis of 4sU-seq and RNA-seq time-course data.

In addition, HTS-flow is using the R BatchJob library to allow running the analysis on a variety of clusters as well as single laptops or desktops.

Other libraries and software used in the pipelines are listed below: