Pinned Repositories
active
Backup of active work
BestPracticesWorkshop
Repository for the workshop "Best practices on development"
Binary-tag
bioconda-recipes
Conda recipes for the bioconda channel.
BlobFish
Differential expression analysis using DEseq2 and Salmon
BootstrapAnn
A tool for computing ASE P values based on ASEReadCounter output files
bravo-protocols
VWorks protocols and other files for the Agilent NGS Workstations at the Genomics facility at SciLifeLab.
Bravo_ST
configs
Config files used to define parameters specific to compute environments at different Institutions
MIP
Mutation Identification Pipeline. Read the latest documentation:
jemten's Repositories
jemten/Bravo_ST
jemten/active
Backup of active work
jemten/BestPracticesWorkshop
Repository for the workshop "Best practices on development"
jemten/Binary-tag
jemten/bioconda-recipes
Conda recipes for the bioconda channel.
jemten/BlobFish
Differential expression analysis using DEseq2 and Salmon
jemten/BootstrapAnn
A tool for computing ASE P values based on ASEReadCounter output files
jemten/bravo-protocols
VWorks protocols and other files for the Agilent NGS Workstations at the Genomics facility at SciLifeLab.
jemten/configs
Config files used to define parameters specific to compute environments at different Institutions
jemten/development
Software development guidelines at Clinical Genomics. http://www.clinicalgenomics.se/development/
jemten/MIP
Mutation Identification Pipeline. Read the latest documentation:
jemten/createpanelrefs
Generate Panel of Normals, models or other similar references from lots of samples
jemten/drop
Pipeline to find aberrant events in RNA-Seq data, useful for diagnosis of rare disorders
jemten/jemt
jemten/MBS
The automated protocols for Spatial transcriptomics
jemten/MegaFusion
Convert RNA fusion files to SV VCF
jemten/mitosign
mtDNA deletion and depletion signatures from wgs data
jemten/modules
Repository to host tool-specific module files for the Nextflow DSL2 community!
jemten/nf_core-tools
Python package with helper tools for the nf-core community.
jemten/python_koans
Python Koans - Learn Python through TDD
jemten/raredisease
Call and score variants from WGS/WES of rare disease patients.
jemten/RareDisease_RNA_workflow
jemten/rnaseq
RNA sequencing analysis pipeline using STAR or HISAT2, with gene counts and quality control
jemten/smrnaseq
Analysis pipeline for small-RNA sequencing data.
jemten/ST_development
Non validated protocols
jemten/SVDB
structural variant database software
jemten/test-datasets
Test data to be used for automated testing with the nf-core pipelines
jemten/TIDDIT
TIDDIT - structural variant calling
jemten/trailblazer
Keep track of and manage analyses
jemten/vcf2cytosure
Convert VCF with structural variations to CytoSure format