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Resources

Here is a list of software, databases and learning material maintained by bioinformatics platform members. More importantly for MDC members and faculty, here is a 1-pager that summarizes all the support services we provide and how to access them.

Databases & Web Apps

doRiNA

DoRiNA is a database for RNA binding protein binding sites and microRNAs.

UCSC browser mirror

We are maintaining a UCSC mirror with limited number of species. You can see reach it via http://genome.mdc-berlin.de. We also provide web space (the link is accessible only from MDC network) for static htmls and Track hub data for UCSC browser. Contact Dan Munteanu for more info.

Internal Galaxy Server

We are maintaining a local version of Galaxy framework available at https://galaxy.mdc-berlin.net/. This website is only accesible within campus. To gain access please send an e-mail to galaxy@mdc-berlin.de. We provide galaxy tutorials as well. These are announced via e-mail using MDC mailling lists.

Software

methylKit

methylKit is an R package for DNA methylation analysis and annotation from high-throughput bisulfite sequencing. The package is designed to deal with sequencing data from RRBS and its variants, but also target-capture methods such as Agilent SureSelect methyl-seq. In addition, methylKit can deal with base-pair resolution data for 5hmC obtained from Tab-seq or oxBS-seq. It can also handle whole-genome bisulfite sequencing data if proper input format is provided.

[https://code.google.com/p/methylkit]

genomation

This is an R package that contains a collection of tools for visualizing and analyzing genome-wide data sets. The package works with a variety of genomic interval file types and enables easy summary and annotation of high throughput data sets with given genomic annotations.

[http://bioinformatics.mdc-berlin.de/genomation/]

RCAS

RNA Centric Annotation System (RCAS) is an R package that provides dynamic annotations with interactive figures and tables for custom input files that contain transcriptomic target regions. Such transcriptomic target regions could be, for instance, peak regions detected by CLIP-Seq analysis that detect protein-RNA interactions, MeRIP-Seq analysis that detect RNA modifications (alias the epitranscriptome), or any collection of target regions at the level of the transcriptome. RCAS overlays the input target regions with the annotated gene features and generates a variety of summary plots. Furthermore, RCAS enables GO term and gene set enrichment analyses based on targeted genes.

[https://github.com/BIMSBbioinfo/RCAS/]

netSmooth

netSmooth is an R/Bioconductor package for network smoothing of single cell RNA sequencing data. Using gene interaction networks such as protein- protein interactions as priors for gene co-expression, netsmooth improves cell type identification from noisy, sparse scRNA-seq data. The smoothing method is suitable for other gene-based omics data sets such as proteomics, copy-number variation, etc.

For a detailed exposition, check out our paper on F1000Research.

[https://github.com/BIMSBbioinfo/netSmooth/]

PiGx

PiGx is a collection of reproducible genomics pipelines. More information can be found at the PiGx website It includes the following pipelines:

  • PiGx BSseq for raw fastq read data of bisulfite experiments
  • PiGx RNAseq for RNAseq samples
  • PiGx scRNAseq for single cell RNA-seq analysis
  • PiGx ChIPseq for reads from ChIPseq experiments
  • PiGx CRISPR for the analysis of sequence mutations in CRISPR-CAS9 targeted amplicon sequencing data
  • PiGx SARS-cov-2 for analysing sequenced wastewater samples and identifying given and emerging lineages of SARS-CoV-2.
github repository

We try to develop software in the open as much as we can. You can reach our repository here:

[https://github.com/BIMSBbioinfo/]

Bioinformatics infrastructure support

The platform has additional IT responsibilities within the framework of bioinformatics infrastructure support. Some of those are listed below for reference.

  • Linux workstation support

  • Customized software installation and packaging with Guix, see list of available bioinformatics software here.

  • Maintain and set up virtual machines running databases and web apps

  • Backups (sequencing data, Linux workstations, puppet data)

  • BIMSB user support: send an e-mail to helpdesk@mdc-berlin.de for IT related requests

    • Unix + Grid Engine trainings, see Training and Learning Materials
    • Processing sequencing data restore requests
    • Cluster problems
    • Triaging file access issues

  • Installation / configuration / maintenance for BIMSB apps servers (the physical machines)

Learning materials

Introduction to Unix and SGE (Sun Grid Engine)

This is a resource maintained and developed by platform members.

[http://bioinformatics.mdc-berlin.de/intro2UnixandSGE/]

Notes on Computational Genomics with R

This is a resource developed by Dr.Akalin. Currently, it includes the basics of R and genomic interval analysis using R/Bioconductor packages. More to be added...

[http://al2na.github.io/compgenr/]