VarmaS's repositories
gvs.github.io
Test web
proj_nordic7k-chip
workflow for parsing nordic7k-chip data and blast reads to reference genome
cyp51_PacBio
PacBio reads analysis and SNP calling workflow for cyp51
RNAseq_Quinoa-seed
Transcriptional regulation of quinoa seed quality
bakta
Rapid & standardized annotation of bacterial genomes & plasmids
Distinct_sequences
Distinct_sequence_generator
RGDB
Resistance Gene Data base Web-server (RGDB_Webserver)
qtl2data
Example data for R/qtl2
MACARON
Multi-bAse Codon-Associated variant Re-annotatiON
MACARON-GenMed-LabEx
Multi-bAse Codon-Associated variant Re-annotatiON (MACARON)
Genome_annotation
These are scripts that I use frequently in genome annotation projects. Some of them have evolved awkwardly so the code is difficult to follw
MetaXcan
MetaXcan software and manuscript
Example_ANNOTATION_Scripts
Parse and annotate WGS samples
WholeGenomeSequencing_Repeat-Mask-Annotation
Scripts to filter False Negatives of variants with in the repeat-masking region, and to add gene expression annotations data
patternCNV
a versatile tool for detecting copy number changes from exome-seq data