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Fayaz Seifuddin's Projects

agat icon agat

Another Gff Analysis Toolkit

airlift icon airlift

AirLift is a tool that updates mapped reads from one reference genome to another. Unlike existing tools, It accounts for regions not shared between the two reference genomes and enables remapping across all parts of the references. Described by Kim et al. (preliminary version at http://arxiv.org/abs/1912.08735)

amazon-ebs-autoscale icon amazon-ebs-autoscale

Don't run out of disk space on your EC2 instance when generating or working with large files. Automatically add EBS volumes to a filesystem mount point in response to disk utilization.

awesome-pipeline icon awesome-pipeline

A curated list of awesome pipeline toolkits inspired by Awesome Sysadmin

aws-shell icon aws-shell

An integrated shell for working with the AWS CLI.

baseset icon baseset

Provides classes for working with sets

bipolar_lncrna icon bipolar_lncrna

Scripts for analyzing and exploring lncRNA in bipolar RNA-Seq data

boomer icon boomer

Print the Output of Intermediate Steps of a Call

celfie icon celfie

cfDNA cell type of origin estimation

cellxgene icon cellxgene

An interactive explorer for single-cell transcriptomics data

cfchip-seq icon cfchip-seq

Code to accompany publication on cell free chromatin immunoprecipitation (cfChIP)

chm13 icon chm13

The complete sequence of a human genome

clustergrammer2 icon clustergrammer2

"Dimensionality-increasing" data visualization tool and interactive WebGL Jupyter widget built for single-cell data.

cwltool icon cwltool

Common Workflow Language reference implementation

datapasta icon datapasta

On top of spaghetti, all covered in cheese....

deepvariant icon deepvariant

DeepVariant is an analysis pipeline that uses a deep neural network to call genetic variants from next-generation DNA sequencing data.

directrna icon directrna

This repository contains scripts used in the dRNA sequencing with Nanopore thesis.

dmrseq icon dmrseq

R package for Inference of differentially methylated regions (DMRs) from bisulfite sequencing

dockerized_tools_and_pipelines icon dockerized_tools_and_pipelines

Contains Dockerfiles for different tools. Docker images will be published as packages and will be associated to this repository

emerald icon emerald

tools to efficiently retrieve and calculate LD

ethseq icon ethseq

Ethnicity Annotation from Whole Exome Sequencing Data

fgsea icon fgsea

Fast Gene Set Enrichment Analysis

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