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Tools


The following is a list of the bioinformatic tools I have developed, or supervised in the development, over the years. You can access them, from the respective links.

aScan

For allele-specific or allele-biased gene transcription from RNA-Seq data

GitHub page

RNentropy

For finding genes with significant variation of expression in multiple conditions (as in "beyond pairwise comparisons")


R implementation at CRAN

Weeder

For finding over-represented sequence motifs in nucleotide sequences, tailored for finding Transcription Factor Binding Sites in promoter sequences from co-regulated or co-expressed genes, or enriched regions in ChIP-Seq (or similar) experiments.


Pscan

Same as above, but it uses descriptors of binding specificity of known transcription factors. I.e., it looks for over-represented motifs according to TRANSFAC and JASPAR matrices.


PscanChIP

Same as above, but it uses descriptors of binding specificity of known transcription factors. I.e., it looks for over-represented motifs according to TRANSFAC and JASPAR matrices and works, instead of gene promoters, on regions derived from large scale ChIP Seq (or similar) experiments.


Cscan

For finding common regulators of a set of co-expressed genes by using a collection of genome-wide ChIP-Seq experiments for TFs and different chromatin features.



WeederH

for finding of conserved nucleotide motifs and regions through comparative genomics, tailored for the analysis of non-coding DNA and the identification of conserved TFBSs or whole enhancers or silencers.


 
Exalign

for aligning gene intron exon structures, and performing BLAST-like database searches based on structural similarity.



RNAProfile

for finding motifs conserved in sequence and secondary structure in RNA sequences.



GeneSyn

for finding conserved gene order throughout multiple genomes.

Source code: contact me