BOL: Related items

GenomeTools: The versatile open source genome analysis software

Jit — Wed, 07 Feb 2018 10:44:18 -0600

The GenomeTools genome analysis system is a free collection of bioinformatics tools (in the realm of genome informatics) combined into a single binary named gt. It is based on a C library named “libgenometools” which consists of several modules.

If you are interested in gene prediction, have a look at GenomeThreader.

Address of the bookmark: http://genometools.org/

EGAD: Ultra-fast functional analysis of gene networks

Rahul Nayak — Fri, 14 Dec 2018 04:10:35 -0600

With the EGAD (Extending ‘Guilt-by-Association’ by Degree) package, we present a series of highly efficient tools to calculate functional properties in networks based on the guilt-by-association principle. These allow rapid controlled comparisons and analyses. Two of the core features are: a function prediction algorithm which is fully vectorized (neighbor_voting), allowing network characterization across even thousands of functional groups to be accomplished in minutes in cross-validation and an analytic determination of the optimal prior to guess candidates genes across multiple functional sets (calculate_multifunc, auc_multifunc).

Address of the bookmark: https://github.com/sarbal/EGAD

Troyanskaya Lab

Tue, 04 Feb 2020 06:40:36 -0600

The goal of our research is to interpret and distill this complexity through accurate analysis and modeling of molecular pathways, particularly those in which malfunctions lead to the manifestation of disease. We are inventing integrative methods for systems-level pathway modeling through integrative analysis of genome-scale datasets. We apply these approaches in studying challenging biological problems, such as how pathways function in diverse cell types and how they change dynamically.

https://function.princeton.edu/

ProteoClade: A taxonomic toolkit for multi-species and metaproteomic analysis

Jit — Wed, 18 Mar 2020 14:27:20 -0500

ProteoClade is a Python library for taxonomic-based annotation and quantification of bottom-up proteomics data. It is designed to be user-friendly, and has been optimized for speed and storage requirements.

ProteoClade helps you analyze two general categories of experiments:

Targeted Database Searches: Experiments in which a limited number of species are defined ahead of time, such as those involving Patient-Derived Xenografts (PDXs) or host-pathogen interactions. Reference protein sequence databases are used for targeted searches (ex: using Mascot, MaxQuant).
De Novo Searches: Experiments in which the organisms are unspecified ahead of time or involve samples of high taxonomic complexity. Mass spectra are analyzed in the absence of a reference database (ex: using PEAKS, PepNovo).

ProteoClade scales from two organisms to every organism in UniProt. Please refer to the complete documentation at proteoclade.readthedocs.io for installation, a user's guide, and examples.

https://journals.plos.org/ploscompbiol/article?id=10.1371/journal.pcbi.1007741

Address of the bookmark: https://github.com/HeldLab/ProteoClade

RNA-seq workflow: gene-level exploratory analysis and differential expression

Jit — Sat, 09 Oct 2021 07:59:23 -0500

Here we walk through an end-to-end gene-level RNA-seq differential expression workflow using Bioconductor packages. We will start from the FASTQ files, show how these were quantified to the reference transcripts, and prepare gene-level count datasets for downstream analysis. We will perform exploratory data analysis (EDA) for quality assessment and to explore the relationship between samples, perform differential gene expression analysis, and visually explore the results.

Address of the bookmark: http://master.bioconductor.org/packages/release/workflows/vignettes/rnaseqGene/inst/doc/rnaseqGene.html

Tools for Differential expression analysis

Abhi — Tue, 08 Nov 2022 03:40:33 -0600

apeglm - https://bioconductor.org/packages/release/bioc/html/apeglm.html

ashr - https://github.com/stephens999/ashr, https://cran.r-project.org/web/packages/ashr/index.html

consensusDE - https://bioconductor.org/packages/release/bioc/html/consensusDE.html

DESeq2 - https://bioconductor.org/packages/release/bioc/html/DESeq2.html

edgeR - https://bioconductor.org/packages/release/bioc/html/edgeR.html

limma - https://kasperdanielhansen.github.io/genbioconductor/html/limma.html https://bioconductor.org/packages/release/bioc/html/limma.html

MetaCycle - https://cran.r-project.org/web/packages/MetaCycle/index.html, https://github.com/gangwug/MetaCycle

RUVSeq - https://bioconductor.org/packages/release/bioc/html/RUVSeq.html

SARTools - https://github.com/PF2-pasteur-fr/SARTools

tximport - https://github.com/mikelove/tximport

Bactopia: a flexible pipeline for complete analysis of bacterial genomes

Abhi — Sat, 08 Jun 2024 16:25:08 -0500

Bactopia is a flexible pipeline for complete analysis of bacterial genomes. The goal of Bactopia is process your data with a broad set of tools, so that you can get to the fun part of analyses quicker!

Bactopia was inspired by Staphopia, a workflow we (Tim Read and myself) released that is targeted towards Staphylococcus aureus genomes. Using what we learned from Staphopia and user feedback, Bactopia was developed from scratch with usability, portability, and speed in mind from the start.

Bactopia uses Nextflow to manage the workflow, allowing for support of many types of environments (e.g. cluster or cloud). Bactopia allows for the usage of many public datasets as well as your own datasets to further enhance the analysis of your sequencing. Bactopia only uses software packages available from Bioconda and Conda-Forge to make installation as simple as possible for all users.

To highlight the use of Bactopia and Bactopia Tools, we performed an analysis of 1,664 public Lactobacillus genomes, focusing on Lactobacillus crispatus, a species that is a common part of the human vaginal microbiome. The results from this analysis are published in mSystems under the title: Bactopia: a flexible pipeline for complete analysis of bacterial genomes

Address of the bookmark: https://bactopia.github.io/latest/

Patterns: a modeling tool dedicated to biological network modeling

Abhimanyu Singh — Fri, 26 Jul 2019 01:11:59 -0500

It is designed to work with patterned data. Famous examples of problems related to patterned data are:

recovering signals in networks after a stimulation (cascade network reverse engineering),
analysing periodic signals.

Address of the bookmark: https://github.com/fbertran/Patterns

Des Higgins: Visualizing Multiple Sequence Alignments

Wed, 26 Feb 2014 00:50:08 -0600

Copyright Broad Institute, 2013. All rights reserved. Des Higgins (http://www.bioinf.ucd.ie) gives a very entertaining introduction to the visualization of multiple sequence alignment, and to his widely-used Clustal tool. He highlights the emerging challenge of managing alignments with a very large number of sequences, and presents several approaches to this challenge, including faster algorithms and abstract views of clusters of alignments. This talk was presented at VIZBI 2011, an international conference series on visualizing biological data (http://www.vizbi.org) funded by NIH & EMBO. For information about data visualization efforts at the Broad Institute, please visit: http://www.broadinstitute.org/node/1363/

deepTools

Martin Jones — Sat, 08 Nov 2014 15:02:08 -0600

deepTools addresses the challenge of handling the large amounts of data that are now routinely generated from DNA sequencing centers. To do so, deepTools contains useful modules to process the mapped reads data to create coverage files in standard bedGraph and bigWig file formats. By doing so, deepTools allows the creation of normalized coverage files or the comparison between two files (for example, treatment and control). Finally, using such normalized and standardized files, multiple visualizations can be created to identify enrichments with functional annotations of the genome.

Publicaton: http://nar.oxfordjournals.org/content/early/2014/05/05/nar.gku365.full

Source Code and Wiki: https://github.com/fidelram/deepTools/wiki

Galaxy Tool Shed repository: http://toolshed.g2.bx.psu.edu/view/bgruening/deeptools

and example Galaxy workflows: http://toolshed.g2.bx.psu.edu/view/bgruening/deeptools_workflows