Bioinformatics software developed in U900 at Institut Curie

                                         

CGH-array, ChIP-chip, ChIP-Seq, SNP (Genome), NGS
Title Description Availability
GLAD Chromosomal breakpoint detection in array CGH experiments (Gain and Loss Analysis of DNA).
Developed by Philippe Hupé et al.		 R package is available either upon request at glad@curie.fr or from bioconductor.
MANOR Normalization of array-CGH data (Micro-Array NORmalization).
Developed by Pierre Neuvial et al.		 R package is available upon request at manor@curie.fr or from bioconductor.
MICSA Transcription factor binding site extraction from ChIP-Seq data by de novo identification of consensus motifs Access to the MICSA software at http://bioinfo-out.curie.fr/projects/micsa.
SVDetect Detection of genomic structural variations from paired-end or mate-pair sequencing data Access to the SVDetect software from sourceforge.
ITALICS An algorithm for normalization and DNA copy number calling for Affymetrix SNP arrays R package is available from bioconductor.
SMETHILLIUM Spatial normalisation METHod for ILLumina InfinIUM HumanMethylation BeadChip Access to the SMETHILLIUM software at http://bioinfo-out.curie.fr/projects/smethillium
FREEC Control-free prediction of copy number alterations in deep-sequencing data using normalization on GC-content.
Developed by Valentina Boeva et al.		 Access to the FREEC software at http://bioinfo-out.curie.fr/projects/freec
                              

Image Analysis
Title Description Availability
MAIA Microarray Automatic Image Analysis Developed by Eugene Novikov et al. The MAIA software is available upon request, contact: maia@curie.fr.
More information is available from the Download :
User Manual (PDF), Demo Images, MAIA 2.5 Demo.
                              

Protein Identification (Proteome)
Title Description Availability
ProMS Proteome analysis using Mass Spectrometry.
Developed by Patrick Poullet et al.		 Access to the on-line demo of ProMS at http://bioinfo.curie.fr/myproms.
The ProMS software will be available upon request very soon.
Contact: proms@curie.fr.
                     

User Interfaces
Title Description Availability
CAPweb Cgh Array analysis Pipeline on the WEB.
Developed by Stéphane Liva et al.		 Access to the CAPweb software at http://bioinfo.curie.fr/CAPweb.
The CAPweb software is available upon request.
Contact: capweb@curie.fr.
VAMP Visualisation and Analysis of CGH arrays, transcriptome and other Molecular Profiles.
Developed by Philippe La Rosa et al.		 VAMP can be run on public sets of data at http://bioinfo.curie.fr/vamp.
The following array-CGH data are currently browsable : Douglas et al. (2004), de Leeuw et al. (2004), Veltman et al. (2003), Pollack et al. (CGH and transcriptome array data, 2002), Snijders et al. (2001) and Nakao et al. (2004).
The VAMP software is available upon request.
Contact: vamp@curie.fr.