Software

Stable

  • fastx-barber (sequencing)
    A Python package to trim and extract flags from FASTA and FASTQ files.
  • GPSeq-RadiCal (sequencing, GPSeq)
    An R script for fast and streamlined Radiality Calculation from GPSeq data. GPSeq-RadiCal aims to provide the same functionalities as the gpseqc Python3 package, but with much lower memory usage and faster computation times.
  • iFISH-probe-design (FISH, oligonucleotides)
    A Python3.6.1+ package containing tools for selection of complementary oligonucleotides to build iFISH probes. It also includes a web interface, which simplifies the procedure by removing any requirement for programming skills.
  • oligo-melting (chemistry, FISH, oligonucleotides)
    A Python package with tools to estimate oligonucleotide duplexes melting temperature. It includes state-of-the-art monovalent (e.g., Na+) and bivalent (Mg2+) ion correction, formamide (or general denaturant) correction, and melting curve estimation.

Beta

  • ifpd2 (FISH, oligonucleotides)
    A Python3.7+ package containing tools for selection of complementary oligonucleotides to build iFISH probes. It is based on our previous ifpd package, but works with a different and more detailed database format, allowing for more precise control on the probe design process. This will replace iFISH-probe-design by providing more refined and advance design options and tools.
  • kman (oligonucleotides, sequencing)
    A Python3.8+ package containing tools for selection of complementary oligonucleotides to build iFISH probes. It is based on our previous ifpd package, but works with a different and more detailed database format, allowing for more precise control on the probe design process.
  • radiantkit (imaging, microscopy)
    Radial Image Analysis Toolkit (RadIAnTkit) is a Python3.8+ package containing tools for full-stack image analysis - from proprietary format conversion to tiff to cellular nuclei segmentation, from the selection of G1 nuclei to the measurement of radial patterns.

Alpha

  • ggkaryo2 (plot, karyotype, ideogram)
    An R package to overlay karyotype and data-track profiles in a ggplot-compatible manner.
  • mnemo-assistant (lab-journal, notes, notebook)
    A Python3.8+ web framework providing tools for journaling and note taking.

Unpackaged & scripts

  • bed-fix-chrom-rearrangement (sequencing, BED, coordinates)
    A Python script that corrects chromosomal rearrangements in bed files. Corrected chromosome sites format checked with assertions. Only first three columns of the bed files are expected and manipulated (i.e., BED3). If present, header track line is preserved and translocation site information are added as “transSite1” and “transSite2”. Corrected bed files are exported with suffix “.transCorrected”.
  • bioTrackBinner (sequencing, binning, biological-data)
    R script to bin biological tracks from different bio-formats into tables conveniently stored in rds files. Supports the following formats: bed, bedGraph, bigWig, cod, txt, xlsx. Custom code can be provided on the fly for currently unsupported or esotic file formats.
  • fqdedup (sequencing, deduplication)
    A Python script for single-ended FASTQ file deduplication
  • wave2color (physics, optics)
    How to get a color (as a hexadecimal string) from a wavelength (nm, in the visible range). A function is provided in the following languages: Python, TypeScript, and Javascript.

Legacy

GPSeq

  • pygpseq (imaging, microscopy, GPSeq, FISH)
    A Python3 package that provides tools to analyze images of GPSeq samples.
  • pygpseq-scripts (imaging, microscopy)
    Scripts that extend the pygpseq package functionalities.
  • gpseq-seq-gg (sequencing, pre-processing, GPSeq)
    A pipeline for Genomic loci Positioning by Sequencing (GPSeq) sequencing data analysis.
  • gpseqc (sequencing, * GPSeq*)
    A Python3 package that provides tools to estimate the 3D spatial nuclear centrality of genomic regions and compare different centrality rankings.
  • gpseqc-snakemake (sequencing, GPSeq, snakemake)
    Snakemake workflow to run GPSeqC pipeline.

FISH

  • oligo-picker (FISH, oligonucleotides)
    Perl5 pipeline for identification of FISHing location-specific oligonucleotide sequences, developed by Mihaela Martis for the Bienko&Crosetto Labs, through the scope of the Bioinformatic Long-term Support (WABI) offered by Science for Life Laboratory (Stockholm, SE).
  • ood-fish (FISH, oligonucleotides, chemistry)
    Orthogonal Oligo Design for Fluorescence In Situ Hybridization (OOD-FISH) is a pipeline for the identification of oligonucleotide sequences that do not hybridize to a reference genome of interest. Such orthogonal oligonucleotides can easily be used as barcodes for PCR or similar protocols.
  • iFISH-singleLocus-analysis (imaging, microscopy, FISH, snakemake)
    Pipeline for iFISH single locus data analysis.

Microscopy

  • SpectraScope (microscopy, optics, fluorophores)
    Interactive interface to visualize spectra and filter sets for any microscope. Easily customizable. The idea behind SpectraScope is to provide users with an easy-to-use web-interface (that can be directly downloaded and run locally) where to visualize fluorophores and microscope filter sets of interest. This can be invaluable when setting up new optical configurations or designing new microscopy-based experiments.

3D structures

Tumor Evolution

  • tepp (cancer, evolution)
    Tumor Evolution Paths Project contains R scripts and classes for efficient manipulation of tumor evolution paths.
  • tema (cancer, visualization, graph)
    Tumor Evolution Manager and Analyzer (v0.3.0)