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r_codes

Complete set of my R codes which I used in different analyses. The list may not be exhaustive

rnaseq_tutorial

Informatics for RNA-seq: A web resource for analysis on the cloud. Educational tutorials and working pipelines for RNA-seq analysis including an introduction to: cloud computing, critical file formats, reference genomes, gene annotation, expression, differential expression, alternative splicing, data visualization, and interpretation.

run-fastqc

Nextflow pipeline to test Singularity and SLURM for H3ABioNet GWAS workshop 2018

saffire

sars-cov-2_rnavariantcalling

scrna_scatac_seq

scRNA and scATAC analysis scripts

scrnaseq_analysis_vignette

Tutorial for scRNA-seq data analysis beginners using R

scvi-tools

Deep probabilistic analysis of single-cell omics data

slugproject

spectralprocessing

This repository contains the information used in pre-processing of the MS/MS spectra and how this can be used to improve the identification of non-human peptides from the raw files

splicify

spritz

Software for RNA-Seq analysis on Windows, including creating sample-specific proteoform databases from genomic data

tbpeptideid

MS/MS database search workflow

telozib

the-world-of-faculty

resources for faculty

tiny-test-data

Super small biological datasets for unit testing

train

A simple Bioconductor package for analysis of proteomics data

trial_dataset_rnaseq

This is a dry run for the RNAseq data analysis in general

trio_binning

Programs implementing the trio-binning genome assembly method

ufs_metagenomics

Pipeline does quality control, assembly and binning

vap

VAP : For Reference mapping and Variant detection.

varcall

Nextflow scripts for doing variant calling on human samples

variant-calling-pipeline

HPC based pipelines for variant calling using GATK

variant-calling-pipeline-gatk4

Variant Calling Pipeline Using GATK4 and Nextflow

verkkonf

wes

xcell

Cell types enrichment analysis

xcms_camera

zebrafish_t2t

Telomere-to-telomere consortium Zebrafish project