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/lncRNAKB
Scripts for analyzing data displayed and deposited on the long non-coding RNA knowledgebase (lncRNAKB)
seifudd/ChIP-Seq_Cut_and_Tag_Cut_and_Run_scripts
Scripts to analyze ChIP-Seq including Cut&Tag and Cut&Run data
seifudd/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.
seifudd/biodocker
docker images for bioinformatics
seifudd/cellxgene
An interactive explorer for single-cell transcriptomics data
seifudd/ChIP-seq-analysis
ChIP-seq analysis notes from Ming Tang
seifudd/CHM13
The complete sequence of a human genome
seifudd/clustergrammer2
"Dimensionality-increasing" data visualization tool and interactive WebGL Jupyter widget built for single-cell data.
seifudd/cornell-cs5785-applied-ml
Teaching materials for the applied machine learning course at Cornell Tech
seifudd/cs-video-courses
List of Computer Science courses with video lectures.
seifudd/cwltool
Common Workflow Language reference implementation
seifudd/docker-cheat-sheet
Docker Cheat Sheet
seifudd/dockerized_tools_and_pipelines
Contains Dockerfiles for different tools. Docker images will be published as packages and will be associated to this repository
seifudd/gggenomes
A grammar of graphics for comparative genomics
seifudd/ggside
ggplot2 extension allowing for plotting various geometries as side panels using the ggplot2 API
seifudd/janggu
Deep learning infrastructure for bioinformatics
seifudd/levioSAM
Lift-over alignments from variant-aware references
seifudd/machine_learning_complete
A comprehensive repository containing 30+ notebooks on learning machine learning!
seifudd/methrix
An R :package: for fast and flexible DNA methylation analysis
seifudd/NanoSplicer
seifudd/neural-admixture
seifudd/P-20210813-0005_I2S_Assay_Development_with_Illumina
I2S Assay Development with Illumina
seifudd/PMR
seifudd/QUILT
seifudd/r-data-recipes
A cookbook of delectable data recipes in R.
seifudd/s3fs-fuse
FUSE-based file system backed by Amazon S3
seifudd/S3V2_IDEAS_ESMP
S3norm ver2 + IDEAS epigenetic state / master peak list
seifudd/s5cmd
Parallel S3 and local filesystem execution tool.
seifudd/scripts
scripts
seifudd/seqQscorer