BgeeCall: generate gene expression calls with BgeeCall

In BgeeDB/BgeeCall: Automatic RNA-Seq present/absent gene expression calls generation

generate gene expression calls with BgeeCall

Description

BgeeCall allows to generate present/absent gene expression calls without using an arbitrary cutoff like TPM<1. Calls are generated based on reference intergenic sequences. These sequences are generated based on expression of all RNA-Seq libraries of each species integrated in Bgee (https://bgee.org).

Details

Thes most important functions are :

• generate_calls_workflow : generate present/absent calls on a computer

• generate_slurm_indexes : generate kallisto indexes for a list of libraries on a cluster with slurm queuing system.

• generate_slurm_calls : generate present/absent calls for a list of libraries on a cluster with slurm queuing system. Indexes have to be generated first with the function 'generate_slurm_indexes'

• merging_libraries : merge calls from different libraries corresponding to the same condition. Extremely useful if different libraries correspond to same condition (e.g. same anatomical entity from same species)

For more details please have a look at the vignette with the command vignette("BgeeCall")

Author(s)

Julien Wollbrett

See Also

https://github.com/BgeeDB/BgeeCall

BgeeDB/BgeeCall documentation built on Nov. 10, 2023, 5:40 a.m.