genomics
A collection of scripts and notes related to genomics and bioinformatics
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- plotPCAWithSampleNames.R
- converting-files.md
- files-chrom-sizes.md
- files-fasta.md
- files-fastq.md
- files-gtf.md
- files-vcf.md
- heatmaps.md
- pathways.md
- r.md
- rna-seq-strand.md
- rna-seq.md
- single-cell-rna-seq.md
- cnv-freec-genome-plot.R
- cnv-freec-heatmap.R
- csv-clean.sh
- fastq-merge.pl
- fastq-quality-bars.sh
- gtf-remove-overlapping.pl
- hdc-1-import-fcs.qmd
- hdc-2-prepare-sce.qmd
- hdc-3-analyze-sce.qmd
- meth-minfi.R
- mut-mhc-binding.pl
- scrna-10x-seurat-1.R
- scrna-10x-seurat-2.R
- scrna-10x-seurat-3.R
- scrna-decontaminate-soupx.R
- scrna-doublets-scdblfinder.R
- snvs-cnvs-mutect-strelka-freec-pyclone.R
- assembly-10x-supernova.sh
- cnvs-wgs-freec.sh
- jupyter.sh
- scrna-10x-cellranger-aggr.sh
- scrna-10x-cellranger-count-features.sh
- scrna-10x-cellranger-count.sh
- scrna-10x-cellranger-multi.sh
- assembly-10x-supernova.sh
- bcl2fastq-sample-sheet-fix.sh
- join-all.sh
- scrna-10x-cellranger-aggr.sh
- scrna-10x-cellranger-count.sh
- wgs-10x-longranger.sh
- draft-genome-init.md
- gatk-mouse-mm10.md
- microarray.md
- nanopore-init.md
- ref-genome-gfp.md
- ref-genome-init.md
- rna-seq-diff-exp.md
- rrna-ref.md
- .gitignore
- README.md
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