Pinned Repositories
akt
Ancestry and Kinship Tools
AnnoProbe
edge-detection
exome_analysis
A pipeline for analysis of exome seq from raw fastq to annotated variants
GSEA_Analysis
quadrantplots
snijesh.github.io
snijesh's Repositories
snijesh/edge-detection
snijesh/ASD_Exome
snijesh/autism_precision_medicine
Nature Medicine paper. A Multidimensional Precision Medicine Approach for Autism Subtype Identification.
snijesh/Awesome-Bioinformatics-Benchmarks
A curated list of bioinformatics bench-marking papers and resources.
snijesh/BC_Intrinsic_subtyping
snijesh/bcbio-nextgen
Validated, scalable, community developed variant calling, RNA-seq and small RNA analysis
snijesh/chipseq
ChIP-seq peak-calling, QC and differential analysis pipeline.
snijesh/clinvap
WIP: A Nextflow pipeline to perform clinical variant annotation and reporting
snijesh/covid_symptoms
snijesh/deepvariant
Google's DeepVariant variant caller as a Nextflow pipeline
snijesh/DGE_workshop
snijesh/E-MTAB-6141
Data from Lewis, Barnes, Blighe et al., Cell Rep. 2019 Aug 27; 28(9): 2455–2470.e5.
snijesh/EnhancedVolcano
Publication-ready volcano plots with enhanced colouring and labeling
snijesh/fastqcr
fastqcr: Quality Control of Sequencing Data
snijesh/gatk-docs
Documentation archive for GATK tools and workflows
snijesh/gatk4-jupyter-notebook-tutorials
This repository contains Jupyter Notebooks containing GATK Best Practices Workflows
snijesh/gdc-rnaseq-tool
Tool to download/merge RNASeq data from the GDC Portal in matrices identified by TCGA barcode
snijesh/goatools
Python library to handle Gene Ontology (GO) terms
snijesh/gwas
A pipeline for Genome Wide Association Studies
snijesh/immunedeconv
A unified interface to immune deconvolution methods (CIBERSORT, EPIC, quanTIseq, TIMER, xCell, MCPcounter)
snijesh/labs
Rmd source files for the HarvardX series PH525x
snijesh/learning_vcf_file
Learning the Variant Call Format
snijesh/methylseq
Methylation (Bisulfite-Sequencing) analysis pipeline using Bismark or bwa-meth + MethylDackel
snijesh/mutation-signatures
Create mutation signatures from MAF's, and decompose them into Stratton signatures
snijesh/pingouin
Statistical package in Python based on Pandas
snijesh/Predict-the-Happiness-HackerEarth-Challenge
It uses 2-layered fully connected/Dense Neural network model to predict whether the hotel reviews at TripAdvisor site are positive sentiment or negative sentiment.
snijesh/RIF-Scores-with-Alternative-Correlation-Measures
snijesh/rnaseq
RNA sequencing analysis pipeline using STAR, HISAT2 and Salmon with gene counts and quality control
snijesh/Shiny-Seq
Shiny-Seq: A web based interactive pipeline to analyze RNA-Seq data
snijesh/smrnaseq
A small-RNA sequencing analysis pipeline