Dalmolin Systems Biology Group

All

29 repositories

euryale
Public
A pipeline for taxonomic classification and functional annotation of metagenomic reads. Based on MEDUSA
snakemake pipeline nextflow diamond metagenomics functional-annotation kaiju taxonomic-classification
Nextflow
•
MIT License
•0•5•0•0•Updated Nov 22, 2024Nov 22, 2024
intro_deep-learning
Public
Jupyter Notebook
•1•4•0•0•Updated Nov 14, 2024Nov 14, 2024
dalmolingroup.github.io
Public
Dalmolin Group's website
HTML
•
BSD 3-Clause "New" or "Revised" License
•4•0•1•1•Updated Nov 11, 2024Nov 11, 2024
curso-shell
Public
Curso de Introdução à Linha de Comando, ministrado como parte da Semana de Portas Abertas do PPg-Bioinfo
TeX
•0•0•0•0•Updated Oct 13, 2024Oct 13, 2024
easylayout
Public
interactive force-directed graph layouts within RStudio
ggplot2 bioinformatics r shiny svelte data-visualization networkx bioconductor graph-theory cytoscape
JavaScript
•
Other
•0•4•2•0•Updated Oct 11, 2024Oct 11, 2024
MB_MRA
Public
R
•1•1•0•0•Updated Oct 1, 2024Oct 1, 2024
bulkrna
Public
Dalmolin Group's workflow for pre-processing, alignment and quantification of bulk RNA-seq data
bioinformatics pipeline nextflow expression bulk-rna-seq
Groovy
•
MIT License
•0•7•0•0•Updated Sep 30, 2024Sep 30, 2024
MEDUSA
Public
Metagenomic pipeline managed by snakemake
Python
•
GNU General Public License v3.0
•3•18•0•0•Updated Sep 18, 2024Sep 18, 2024
mdd-paper
Public
Sex-specific transcriptional alteration profile of MDD
R
•1•0•0•0•Updated Aug 16, 2024Aug 16, 2024
cochineal_16s
Public
Analysis of 16S data on the cochineal insect
metagenomics 16s cochineal metataxonomics
TeX
•0•0•0•0•Updated Aug 6, 2024Aug 6, 2024
.github
Public
MIT License
•0•0•0•0•Updated Jun 22, 2024Jun 22, 2024
trastuzumab_dge
Public
DGE for trastuzumab-treated expression datasets
HTML
•0•1•0•0•Updated May 27, 2024May 27, 2024
intro-single-cell
Public
Introduction to single-cell RNA-seq analysis
R
•
MIT License
•2•2•0•0•Updated May 15, 2024May 15, 2024
MicroView
Public
A reporting tool for aggregating results from taxonomic classification analyses
reporting metagenomics taxonomic-classification taxonomic
Python
•
BSD 3-Clause "New" or "Revised" License
•0•0•0•0•Updated May 2, 2024May 2, 2024
Network-lncRNA-mCRPC
Public
Scripts used in the analyzes of the paper titled "Revealing metastatic castration-resistant prostate cancer (mCRPC) master regulator through lncRNA-centered regulatory network".
R
•0•2•0•0•Updated Jul 25, 2023Jul 25, 2023
meta_taraoceans
Public
Bioinformatics research project on metagenomic in samples from TaraOceans expediction
R
•1•1•0•0•Updated Jun 7, 2023Jun 7, 2023
KeggPathwayAPs
Public
Systems Biology Approaches in the Investigation of Articulation Points in Kegg Metabolic Pathways
R
•
GNU General Public License v3.0
•0•2•0•0•Updated Jun 6, 2022Jun 6, 2022
KEGG-Pathway-Viewer
Public
Tool to visualize KEGG networks
HTML
•
MIT License
•1•0•0•0•Updated Feb 17, 2022Feb 17, 2022
MEDUSA_supplements
Public
A hub for information related to the manuscript "MEDUSA: A Pipeline for Sensitive Taxonomic Classification and Flexible Functional Annotation of Metagenomic Shotgun Sequences"
0•0•0•0•Updated Jan 30, 2022Jan 30, 2022
ComparisonMEGANxMEDUSA
Public
R
•2•0•0•0•Updated Jan 29, 2022Jan 29, 2022
transcriptogramer
Public
R package for transcriptional analysis based on transcriptograms
R
•3•1•0•0•Updated Sep 14, 2021Sep 14, 2021
annotate
Public
Python script to annotate each query using the best alignment for which a mapping is known
python leveldb diamond alignment
Python
•
GNU General Public License v3.0
•1•1•0•0•Updated Aug 18, 2021Aug 18, 2021
essential_genes_paper
Public
Repository for the ancestry analysis of essential genes in eukaryotes
essential-genes systems-evolution
R
•1•0•0•0•Updated Jun 2, 2021Jun 2, 2021
ewing-mra-netinfer
Public
R
•0•2•0•0•Updated Apr 2, 2021Apr 2, 2021
neurotransmissionevolution
Public
Research compendium for Viscardi et al, 2020.
bioinformatics r evolution network-analysis kegg igraph orthology expression-atlas research-compendium stringdb
TeX
•2•4•0•0•Updated Aug 25, 2020Aug 25, 2020
LeadNPC
Public
Systems Biology-Based Analysis Indicates Global Transcriptional Impairment in Lead-Treated Human Neural Progenitor Cells
R
•
GNU General Public License v3.0
•0•0•0•0•Updated Aug 20, 2020Aug 20, 2020
geneplast.data.string.v110
Public
R
•0•0•0•0•Updated Apr 9, 2020Apr 9, 2020
gene-regulatory-networks
Public
R
•1•1•0•0•Updated Oct 22, 2019Oct 22, 2019
seriation
Public
C code to find a suitable linear order for a set of proteins
c protein ordering seriation
C
•1•0•0•0•Updated May 6, 2019May 6, 2019