Published July 2, 2024
| Version v1
Software documentation
Open
Code generated to analyze the dynamics of Orsay virus accumulation and the C. elegans responses within the course of an infection
-
1.
Institute for Integrative Systems Biology
Contributors
Project leader:
-
1.
Institute for Integrative Systems Biology
-
2.
Santa Fe Institute
Description
A) PREPROCESS AND ALIGN READS (preDEA)
- Preprocess fastq files with
bbduk.sh:preprocessOrV.sh - Align and quantify gene expression with
STAR:alignN2.sh
B) Differential Expression Analysis and related
- Create count matrix from individual STAR count files:
prepareCountMatrix.R - DEA:
DEA.R - Correlated/anticorrelated genes:
correlationLog2FCwVirus.R - Comparison analysis:
comparisonAnalysis.R
C) VISUALIZATION: code to create the plots
- Main figures:
fig1.R,fig2.R,fig3.R,fig4.R,fig5.Randfig6.R
Files
OrV_progression-main.zip
Files
(30.1 kB)
| Name | Size | Download all |
|---|---|---|
|
md5:efea672189519ff74f30680be2e79548
|
30.1 kB | Preview Download |
Additional details
Identifiers
Funding
- Agencia Estatal de Investigación
- InHAVEN PID2022-136912NB-I00
- Generalitat Valenciana
- HAVEN CIPROM/2022/59
- Agencia Estatal de Investigación
- Juan de la Cierva FJC2021-047264-I
- Ministerio de Ciencia, Innovación y Universidades
- Formación Profesorado Universitario FPU2019/05246
- Ministerio de Ciencia, Innovación y Universidades
- Formación Profesorado Universitario FPU2021/00410
- Generalitat Valenciana
- Formación Personal Investigador ACIF/2021/296
- European Space Agency
- SpaceWorms 4000135960/21/NL/GLC/my
Software
- Repository URL
- https://git.csic.es/sfelenalab/OrV_progression
- Programming language
- R
- Development Status
- Active