![\"\"](\"https:\/\/southgreenplatform.github.io\/trainings\/\/images\/trainings-rnaseq.png\")
\n<\/td>\nRNASeq analyses (using Galaxy and TOGGLe)<\/h1>\n
\nThis course offers an introduction to RNASeq analyses using two different workflow management systems: Galaxy and TOGGLe. This includes reference-based mapping, estimates of transcript levels, differential expression (DE) analyses, visualization of statistics results.\n<\/td>\n<\/tr>\n<\/table>\n
Prerequisites<\/h3>\n
Workflow management system (Galaxy, TOGGLe)<\/p>\n
\nProgram<\/h3>\n
Program<\/h3>\n\n- Pseudo-mapping RNASeq reads against a reference transcriptome by using with kallisto (Galaxy) <\/li>\n
- Mapping RNASeq reads against an annotated reference genome with Hisat2 (TOGGLe) <\/li>\n
- Counting reads in transcrits\/genes with Stringtie (TOGGLe) <\/li>\n
- Differential expression analysis using EdgeR and DESeq2 (Pivot and R) <\/li>\n
- Plots, clustering, co-expression network: degust, WGCNA (R and Galaxy) <\/li>\n<\/ul>\n<\/div>\n\n
Learning objectives<\/h3>\n\n- Manipulate packages\/tools available for searching DE genes <\/li>\n
- Think about different normalisation methods<\/li>\n
- Detect differentially expressed genes<\/li>\n
- Compare results between approaches<\/li>\n<\/ul>\n<\/div>\n\n
Training material<\/h3>\n\n- Slides : see<\/a><\/li>\n
- Practice : see<\/a> <\/li>\n<\/ul>\n<\/div>\n\n
Instructors<\/h3>\n\n- Julie Orjuela (JO) - julie.orjuela@ird.fr<\/li>\n
- Aurore Comte (AC) - aurore.compte@ird.fr<\/li>\n
- Gautier Sarah (GS) - gautier.sarah@cirad.fr<\/li>\n
- Catherine Br\u00e9ton (CB) - c.breton@cgiar.org<\/li>\n
- Christine Tranchant (CT) - christine.tranchant@ird.fr<\/li>\n
- Sebastien Ravel (SR) - sebastien.ravel@cirad.fr <\/li>\n
- Alexis Dereeper (AD) - alexis.dereeper@ird.fr <\/li>\n
- Sebastien Cunnac (SC) - sebastien.cunnac@ird.fr <\/li>\n<\/ul>\n<\/div>\n
Trainings<\/h3>\n
\n\n\nDate<\/strong><\/th>\nLocation<\/strong><\/th>\nTopics<\/strong><\/th>\nParrticipants<\/strong><\/th>\nInstructors<\/strong><\/th>\nLinks<\/strong><\/th>\nUnits<\/strong><\/th>\n<\/tr>\n<\/thead>\n\n\n2019<\/td>\n Montpellier, France<\/td>\n Introduction to transcriptomics analyses<\/td>\n 20<\/td>\n JO, CB, GS, SC, AC<\/td>\n <\/td>\n UMR DIADE, IPME, AGAP, Bioversity<\/td>\n<\/tr>\n \n2018<\/td>\n Montpellier, France<\/td>\n Introduction to transcriptomics analyses<\/td>\n 20<\/td>\n CT, SR, AD, SC<\/td>\n <\/td>\n UMR DIADE, IPME, BGPI<\/td>\n<\/tr>\n \n2016<\/td>\n Ouagadougou, Burkina<\/td>\n Bioinformatics applied to genomics<\/td>\n 20<\/td>\n CT, AD<\/td>\n <\/td>\n IRD<\/td>\n<\/tr>\n \n2015<\/td>\n Hanoi, Vietnam<\/td>\n Bioinformatics applied to genomics<\/td>\n 20<\/td>\n AD<\/td>\n <\/td>\n LMI Rice<\/td>\n<\/tr>\n \n2014<\/td>\n Dakar, Senegal<\/td>\n Bioinformatics applied to genomics<\/td>\n 20<\/td>\n CT, AD<\/td>\n <\/td>\n IRD, Bel Air Campus<\/td>\n<\/tr>\n<\/tbody>\n<\/table>\n","protected":false},"excerpt":{"rendered":"
\nLearning objectives<\/h3>\n
Learning objectives<\/h3>\n\n- Manipulate packages\/tools available for searching DE genes <\/li>\n
- Think about different normalisation methods<\/li>\n
- Detect differentially expressed genes<\/li>\n
- Compare results between approaches<\/li>\n<\/ul>\n<\/div>\n\n
Training material<\/h3>\n\n- Slides : see<\/a><\/li>\n
- Practice : see<\/a> <\/li>\n<\/ul>\n<\/div>\n\n
Instructors<\/h3>\n\n- Julie Orjuela (JO) - julie.orjuela@ird.fr<\/li>\n
- Aurore Comte (AC) - aurore.compte@ird.fr<\/li>\n
- Gautier Sarah (GS) - gautier.sarah@cirad.fr<\/li>\n
- Catherine Br\u00e9ton (CB) - c.breton@cgiar.org<\/li>\n
- Christine Tranchant (CT) - christine.tranchant@ird.fr<\/li>\n
- Sebastien Ravel (SR) - sebastien.ravel@cirad.fr <\/li>\n
- Alexis Dereeper (AD) - alexis.dereeper@ird.fr <\/li>\n
- Sebastien Cunnac (SC) - sebastien.cunnac@ird.fr <\/li>\n<\/ul>\n<\/div>\n
Trainings<\/h3>\n
\n\n\nDate<\/strong><\/th>\nLocation<\/strong><\/th>\nTopics<\/strong><\/th>\nParrticipants<\/strong><\/th>\nInstructors<\/strong><\/th>\nLinks<\/strong><\/th>\nUnits<\/strong><\/th>\n<\/tr>\n<\/thead>\n\n\n2019<\/td>\n Montpellier, France<\/td>\n Introduction to transcriptomics analyses<\/td>\n 20<\/td>\n JO, CB, GS, SC, AC<\/td>\n <\/td>\n UMR DIADE, IPME, AGAP, Bioversity<\/td>\n<\/tr>\n \n2018<\/td>\n Montpellier, France<\/td>\n Introduction to transcriptomics analyses<\/td>\n 20<\/td>\n CT, SR, AD, SC<\/td>\n <\/td>\n UMR DIADE, IPME, BGPI<\/td>\n<\/tr>\n \n2016<\/td>\n Ouagadougou, Burkina<\/td>\n Bioinformatics applied to genomics<\/td>\n 20<\/td>\n CT, AD<\/td>\n <\/td>\n IRD<\/td>\n<\/tr>\n \n2015<\/td>\n Hanoi, Vietnam<\/td>\n Bioinformatics applied to genomics<\/td>\n 20<\/td>\n AD<\/td>\n <\/td>\n LMI Rice<\/td>\n<\/tr>\n \n2014<\/td>\n Dakar, Senegal<\/td>\n Bioinformatics applied to genomics<\/td>\n 20<\/td>\n CT, AD<\/td>\n <\/td>\n IRD, Bel Air Campus<\/td>\n<\/tr>\n<\/tbody>\n<\/table>\n","protected":false},"excerpt":{"rendered":"
\nTraining material<\/h3>\n
Training material<\/h3>\n\n- Slides : see<\/a><\/li>\n
- Practice : see<\/a> <\/li>\n<\/ul>\n<\/div>\n\n
Instructors<\/h3>\n\n- Julie Orjuela (JO) - julie.orjuela@ird.fr<\/li>\n
- Aurore Comte (AC) - aurore.compte@ird.fr<\/li>\n
- Gautier Sarah (GS) - gautier.sarah@cirad.fr<\/li>\n
- Catherine Br\u00e9ton (CB) - c.breton@cgiar.org<\/li>\n
- Christine Tranchant (CT) - christine.tranchant@ird.fr<\/li>\n
- Sebastien Ravel (SR) - sebastien.ravel@cirad.fr <\/li>\n
- Alexis Dereeper (AD) - alexis.dereeper@ird.fr <\/li>\n
- Sebastien Cunnac (SC) - sebastien.cunnac@ird.fr <\/li>\n<\/ul>\n<\/div>\n
Trainings<\/h3>\n
\n\n\nDate<\/strong><\/th>\nLocation<\/strong><\/th>\nTopics<\/strong><\/th>\nParrticipants<\/strong><\/th>\nInstructors<\/strong><\/th>\nLinks<\/strong><\/th>\nUnits<\/strong><\/th>\n<\/tr>\n<\/thead>\n\n\n2019<\/td>\n Montpellier, France<\/td>\n Introduction to transcriptomics analyses<\/td>\n 20<\/td>\n JO, CB, GS, SC, AC<\/td>\n <\/td>\n UMR DIADE, IPME, AGAP, Bioversity<\/td>\n<\/tr>\n \n2018<\/td>\n Montpellier, France<\/td>\n Introduction to transcriptomics analyses<\/td>\n 20<\/td>\n CT, SR, AD, SC<\/td>\n <\/td>\n UMR DIADE, IPME, BGPI<\/td>\n<\/tr>\n \n2016<\/td>\n Ouagadougou, Burkina<\/td>\n Bioinformatics applied to genomics<\/td>\n 20<\/td>\n CT, AD<\/td>\n <\/td>\n IRD<\/td>\n<\/tr>\n \n2015<\/td>\n Hanoi, Vietnam<\/td>\n Bioinformatics applied to genomics<\/td>\n 20<\/td>\n AD<\/td>\n <\/td>\n LMI Rice<\/td>\n<\/tr>\n \n2014<\/td>\n Dakar, Senegal<\/td>\n Bioinformatics applied to genomics<\/td>\n 20<\/td>\n CT, AD<\/td>\n <\/td>\n IRD, Bel Air Campus<\/td>\n<\/tr>\n<\/tbody>\n<\/table>\n","protected":false},"excerpt":{"rendered":"
\nInstructors<\/h3>\n
Instructors<\/h3>\n\n- Julie Orjuela (JO) - julie.orjuela@ird.fr<\/li>\n
- Aurore Comte (AC) - aurore.compte@ird.fr<\/li>\n
- Gautier Sarah (GS) - gautier.sarah@cirad.fr<\/li>\n
- Catherine Br\u00e9ton (CB) - c.breton@cgiar.org<\/li>\n
- Christine Tranchant (CT) - christine.tranchant@ird.fr<\/li>\n
- Sebastien Ravel (SR) - sebastien.ravel@cirad.fr <\/li>\n
- Alexis Dereeper (AD) - alexis.dereeper@ird.fr <\/li>\n
- Sebastien Cunnac (SC) - sebastien.cunnac@ird.fr <\/li>\n<\/ul>\n<\/div>\n
Trainings<\/h3>\n
\n\n\nDate<\/strong><\/th>\nLocation<\/strong><\/th>\nTopics<\/strong><\/th>\nParrticipants<\/strong><\/th>\nInstructors<\/strong><\/th>\nLinks<\/strong><\/th>\nUnits<\/strong><\/th>\n<\/tr>\n<\/thead>\n\n\n2019<\/td>\n Montpellier, France<\/td>\n Introduction to transcriptomics analyses<\/td>\n 20<\/td>\n JO, CB, GS, SC, AC<\/td>\n <\/td>\n UMR DIADE, IPME, AGAP, Bioversity<\/td>\n<\/tr>\n \n2018<\/td>\n Montpellier, France<\/td>\n Introduction to transcriptomics analyses<\/td>\n 20<\/td>\n CT, SR, AD, SC<\/td>\n <\/td>\n UMR DIADE, IPME, BGPI<\/td>\n<\/tr>\n \n2016<\/td>\n Ouagadougou, Burkina<\/td>\n Bioinformatics applied to genomics<\/td>\n 20<\/td>\n CT, AD<\/td>\n <\/td>\n IRD<\/td>\n<\/tr>\n \n2015<\/td>\n Hanoi, Vietnam<\/td>\n Bioinformatics applied to genomics<\/td>\n 20<\/td>\n AD<\/td>\n <\/td>\n LMI Rice<\/td>\n<\/tr>\n \n2014<\/td>\n Dakar, Senegal<\/td>\n Bioinformatics applied to genomics<\/td>\n 20<\/td>\n CT, AD<\/td>\n <\/td>\n IRD, Bel Air Campus<\/td>\n<\/tr>\n<\/tbody>\n<\/table>\n","protected":false},"excerpt":{"rendered":"
Trainings<\/h3>\n
Date<\/strong><\/th>\n| Location<\/strong><\/th>\n | Topics<\/strong><\/th>\n | Parrticipants<\/strong><\/th>\n | Instructors<\/strong><\/th>\n | Links<\/strong><\/th>\n | Units<\/strong><\/th>\n<\/tr>\n<\/thead>\n\n | 2019<\/td>\n | Montpellier, France<\/td>\n | Introduction to transcriptomics analyses<\/td>\n | 20<\/td>\n | JO, CB, GS, SC, AC<\/td>\n | <\/td>\n | UMR DIADE, IPME, AGAP, Bioversity<\/td>\n<\/tr>\n | 2018<\/td>\n | Montpellier, France<\/td>\n | Introduction to transcriptomics analyses<\/td>\n | 20<\/td>\n | CT, SR, AD, SC<\/td>\n | <\/td>\n | UMR DIADE, IPME, BGPI<\/td>\n<\/tr>\n | 2016<\/td>\n | Ouagadougou, Burkina<\/td>\n | Bioinformatics applied to genomics<\/td>\n | 20<\/td>\n | CT, AD<\/td>\n | <\/td>\n | IRD<\/td>\n<\/tr>\n | 2015<\/td>\n | Hanoi, Vietnam<\/td>\n | Bioinformatics applied to genomics<\/td>\n | 20<\/td>\n | AD<\/td>\n | <\/td>\n | LMI Rice<\/td>\n<\/tr>\n | 2014<\/td>\n | Dakar, Senegal<\/td>\n | Bioinformatics applied to genomics<\/td>\n | 20<\/td>\n | CT, AD<\/td>\n | <\/td>\n | IRD, Bel Air Campus<\/td>\n<\/tr>\n<\/tbody>\n<\/table>\n","protected":false},"excerpt":{"rendered":" | |
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