siavashmoghadami Goto Github PK

alphafold

Open source code for AlphaFold.

bican

biocstickers

Stickers for some Bioconductor packages - feel free to contribute and/or modify.

bowtie2

A fast and sensitive gapped read aligner

bustools

Tools for working with BUS files

cebpbeta_project_chipseq

cellranger

10x Genomics Single Cell 3' Gene Expression and VDJ Assembly

cellranger-atac

colabfold

Making Protein folding accessible to all via Google Colab!

complete-python-3-bootcamp

Course Files for Complete Python 3 Bootcamp Course on Udemy

deepcell-tf

Deep Learning Library for Single Cell Analysis

hdf5-rust

HDF5 for Rust

kallisto

Near-optimal RNA-Seq quantification

kallistobustools

kallisto | bustools workflow for pre-processing single-cell RNA-seq data

kb_python

A wrapper for the kallisto | bustools workflow for single-cell RNA-seq pre-processing

macs

MACS -- Model-based Analysis of ChIP-Seq

magnetproject_bulkrnaseq

pyrosetta.notebooks

Jupyter Notebooks for learning the PyRosetta platform for biomolecular structure prediction and design

rosettafold

This package contains deep learning models and related scripts for RoseTTAFold

rust-pseudoaligner

Single-Cell RNA-seq pseudo-aligner

scanpy

Single-Cell Analysis in Python. Scales to >1M cells.

seurat

R toolkit for single cell genomics

siavashmoghadami.github.io

sleuth

Differential analysis of RNA-Seq

sra-tools

SRA Tools

st_pipeline

ST Pipeline contains the tools and scripts needed to process and analyze the raw files generated with the Spatial Transcriptomics method in FASTQ format.

st_spot_detector

A web tool to do automatic spots detections and positional adjustments for Spatial Transcriptomics Datasets.

star

RNA-seq aligner

trimmomatic

xeus-cling

Jupyter kernel for the C++ programming language