Pinned Repositories
AGAT
Another Gff Analysis Toolkit
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
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.
bipolar_lncRNA
Scripts for analyzing and exploring lncRNA in bipolar RNA-Seq data
cfMethylome
cfDNA Methylation Analysis
ChIP-Seq_Cut_and_Tag_Cut_and_Run_scripts
Scripts to analyze ChIP-Seq including Cut&Tag and Cut&Run data
lncRNAKB
Scripts for analyzing data displayed and deposited on the long non-coding RNA knowledgebase (lncRNAKB)
MethylSeq_and_RNASeq_cortisol_analysis
Scripts for analyzing MethylSeq and RNASeq cortisol data
PGRScorer
Scripts and files to calculate polygenic/genomic risk scores
SMURF-JCVI
seifudd's Repositories
seifudd/PGRScorer
Scripts and files to calculate polygenic/genomic risk scores
seifudd/AGAT
Another Gff Analysis Toolkit
seifudd/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)
seifudd/bipolar_lncRNA
Scripts for analyzing and exploring lncRNA in bipolar RNA-Seq data
seifudd/cfMethylome
cfDNA Methylation Analysis
seifudd/MethylSeq_and_RNASeq_cortisol_analysis
Scripts for analyzing MethylSeq and RNASeq cortisol data
seifudd/aws-shell
An integrated shell for working with the AWS CLI.
seifudd/bioinformatics-one-liners
Bioinformatics one liners from Ming Tang
seifudd/boomer
Print the Output of Intermediate Steps of a Call
seifudd/cfChIP-seq
Code to accompany publication on cell free chromatin immunoprecipitation (cfChIP)
seifudd/datapasta
On top of spaghetti, all covered in cheese....
seifudd/deepvariant
DeepVariant is an analysis pipeline that uses a deep neural network to call genetic variants from next-generation DNA sequencing data.
seifudd/directRNA
This repository contains scripts used in the dRNA sequencing with Nanopore thesis.
seifudd/EthSEQ
Ethnicity Annotation from Whole Exome Sequencing Data
seifudd/fgsea
Fast Gene Set Enrichment Analysis
seifudd/Folder-Structure-Conventions
Folder / directory structure options and naming conventions for software projects
seifudd/freddie
Freddie: Annotation-independent detection and discovery of transcriptomic alternative splicing isoforms using long-read sequencing
seifudd/GAUSS
Gene-set Association analysis Using Sparse Signals
seifudd/genewalk
GeneWalk identifies relevant gene functions for a biological context using network representation learning
seifudd/getting-started-with-genomics-tools-and-resources
Unix, R and python tools for genomics and data science
seifudd/kraken2
The second version of the Kraken taxonomic sequence classification system
seifudd/megadepth
BigWig and BAM utilities
seifudd/NanoMethPhase
Methylation Phasing for Nanopore Sequencing
seifudd/og-aws
📙 Amazon Web Services — a practical guide
seifudd/scRNAseq-analysis-notes
scRNAseq analysis notes from Ming Tang
seifudd/SQANTI3
Repository of SQANTI3 tool for Quality Control of Long-Read Defined Transcriptomes
seifudd/tama
Transcriptome Annotation by Modular Algorithms (for long read RNA sequencing data)
seifudd/tidybulk
Brings transcriptomics to the tidyverse
seifudd/tidylog
Tidylog provides feedback about dplyr and tidyr operations. It provides wrapper functions for the most common functions, such as filter, mutate, select, and group_by, and provides detailed output for joins.
seifudd/TransPi
TransPi – a comprehensive TRanscriptome ANalysiS PIpeline for de novo transcriptome assembly