Valen Group | Tools

Ribosome profiling

shoelaces – is a tool for processing ribosome profiling data. It reads files of mapped reads and 1) filters noise, 2) produces tracks with sub-codon resolution and 3) calculate statistics over a gene set.

CRISPR/Cas9 Genome engineering

CHOPCHOP – is a web tool for selecting the optimum target sites for  CRISPR/Cas9- or TALEN-directed mutagenesis. Available as both a webtool and for the command line version can be found here.

ampliCan – is an R library for assessing cut rates using next generation sequencing. It produces summary statistics and plots. It supports mixtures of amplicons and multiplexed libraries.

Motif Discovery

MoAn – Motif Annealer is a discriminatory motif discovery tool. It uses suffix arrays to rapidly contrast a positive set with a negative set to discover the maximally discriminatory position specific scoring matrix (PSSM).

JASPAR – The largest open database of transcription factor binding site motifs. Created and maintained by the Sandelin lab.

Nanopore Tools

tailfindr – is an R tool that allows the direct estimation of poly(A) tail length from raw data produced by Oxford Nanopore (ONT) RNA or cDNA sequencing approaches.