diff --git a/README.md b/README.md index 6e1df6be39d7c8688b41abfc5b2dc8c80951b206..23569f56d6d42af0665d8dfa8b9d051f891a4c61 100644 --- a/README.md +++ b/README.md @@ -4,32 +4,36 @@ ## Introduction -Focus on exact 5'-end and/or 3'-end quantification of RNAs *via* targeted RNA-Seq. +The EMOTE-tk R library focuses on exact 5'-end and/or 3'-end quantification of RNAs *via* targeted RNA-Seq. Features: -* demultiplexing -* UMI -* filtering and normalisation -* differential proportion statistical analysis -* post-transccriptional modifications quantification and analysis -* signal periodicity analysis -* plotting functions? +* Pre-processing raw reads fastq file + * reads parsing and valitation + * reads feature extraction + * demultiplexing into separate fastq files +* Unique Molecule Identifiers (UMI) +* Wrapper for mapping and quantification of 5'-end or 3'-end of mapped reads +* Post-processing of count table + * filtering and normalisation +* Downstream analysis + * Transcription start sites (TSS) identification + * Signal periodicity analysis + * Post-transccriptional modifications quantification + * Differential proportion statistical analysis Applications: * TSS identification → tuto -* differential 5'-end phosphorylation state analysis +* Endoribonucleolytic cleavage sites identification → tuto * co-translational degradation -* post-transcriptional modification analysis → [tuto](scripts/MenT1.Xu.2023.ipynb) - - +* post-transcriptional modification & differential proportion analysis → [tuto](scripts/Post-transcriptional.modifications.and.differential.proportion.analysis.Xu-2023.ipynb) ## Installation We recommend the use a [mamba](https://mamba.readthedocs.io/) (or conda) environment to ensure proper execution of all the features. -`mamba env create --file src/emote-tk-shared-env-R4.3.2.txt -n your_env_name` +`mamba env create --file src/emote-tk-env.txt -n emote-tk` -`mamba activate your_env_name` +`mamba activate emote-tk` ### Requirements and dependecies @@ -45,15 +49,6 @@ We recommend the use a [mamba](https://mamba.readthedocs.io/) (or conda) environ * VGAM 1.1_9 * survcomp 1.52.0 - -## FAQ - -## Bugs - -## Citation - -## Licence - ## Authors * Roland Barriot diff --git a/src/emote-tk-shared-env-R4.3.2.txt b/src/emote-tk-env.txt similarity index 100% rename from src/emote-tk-shared-env-R4.3.2.txt rename to src/emote-tk-env.txt