edoardo pedrini's repositories
cell_proliferation_longitudinal_study
automatic system to measure the proliferation of the cell (longitudinal study) in a 384 well plate
pipeline-vessel-analysis
the aim of the pipeline is to automate the detection of the vessel and extract information.
TCGA_analysis_stage_vs_expression
the code match the staging of the tumor with the expression data for a gene of interest and perform an ANOVA in order to identify statistically significant differeces
THP-1_polarization
workflow to produce the report of the polarization of THP-1 shRNASET2
tube_assay_formation_analysis
extract and analyze relevant information from tube formation assay images (epi-fluorescent microscopy)
220408_PN0305_ECFC_BMP9_Jess
This is the repo for the reanalysis of the bulk RNAseq data of the BMP9 treated ECFCs in 3D.
230530_brainage
Repository for the analysis of brainage from BrainageR estimates.
240326_lanni_proteomic_mice_CSF
repository for the analysis of the proteomic dataset produced by Prof. Lanni
ascend
R package - Analysis of Single Cell Expression, Normalisation and Differential expression (ascend)
240517_PN0557_BMP9_shear_stress
Repository for the analysis of the dataset with ECFCs treated with BMP9 or vehicle and shear stress
240522_clustering_MS_imaging
Repository for the collaborative work on MS imaging analysis
bioinformatics
:microscope: Path to a free self-taught education in Bioinformatics!
BS_run_04
Repository for the analysis fo the Brain Speheres dataset, run 04
fluorescence-simulator
A simple ImageJ plugin to simulate blur and noise from fluorescence imaging
IPA4LSx
ImageJ Macro Scripts showcased during Image Processing and Analysis for Life Scientists MOOC on EdX
merfish_sample_R
sample script to load and explore merfish dataset
query_transcription_factor_db
example of how to perform a query to TRANSFAC and JSPAR from R
retinal_vascular_image_analysis
macro used to perform image analysis of the retina
single_cell_analysis
step followed to analyze the single cell qPCR data from Biomark, without singular analysis toolset
test_liana
this repository contains the script and test for analyzing CCC using the LIANA package https://saezlab.github.io/liana/
test_MOFA
repository with testing some functionality of MOFA https://biofam.github.io/MOFA2/
test_raptor
repository for test-script for running RAPToR https://www.nature.com/articles/s41592-022-01540-0
test_SingleR
repo for sample scripts for the implementation of the different functionalities available from SingleR http://bioconductor.org/books/release/SingleRBook/introduction.html
TEtranscripts
A package for including transposable elements in differential enrichment analysis of sequencing datasets.
tool_testing_clusterHSR
repo for the sample script used for testing packages