cfarkas

cfarkas's Stars

• facebookresearch/segment-anything

  The repository provides code for running inference with the SegmentAnything Model (SAM), links for downloading the trained model checkpoints, and example notebooks that show how to use the model.

  Language:Jupyter Notebook46.8k3066625.5k

• DeepLabCut/DeepLabCut

  Official implementation of DeepLabCut: Markerless pose estimation of user-defined features with deep learning for all animals incl. humans

  Language:Python4.5k1261.9k1.6k

• neurobin/shc

  Shell script compiler

  Language:C2k76130338

• OpenGene/fastp

  An ultra-fast all-in-one FASTQ preprocessor (QC/adapters/trimming/filtering/splitting/merging...)

  Language:C++1.9k49513332

• Project-MONAI/tutorials

  MONAI Tutorials

  Language:Jupyter Notebook1.8k33632668

• lh3/seqtk

  Toolkit for processing sequences in FASTA/Q formats

  Language:C1.4k62172309

• sqjin/CellChat

  R toolkit for inference, visualization and analysis of cell-cell communication from single-cell data

  Language:R62314727142

• cov-lineages/pangolin

  Software package for assigning SARS-CoV-2 genome sequences to global lineages.

  Language:Python42645381108

• mousepixels/sanbomics_scripts

  scripts and notebooks from sanbomics

  Language:Jupyter Notebook3391123130

• lh3/miniprot

  Align proteins to genomes with splicing and frameshift

  Language:C31775617

• morris-lab/CellOracle

  This is the alpha version of the CellOracle package

  Language:Python299720650

• statOmics/tradeSeq

  TRAjectory-based Differential Expression analysis for SEQuencing data

  Language:HTML237724827

• IanevskiAleksandr/sc-type

  Language:HTML22156144

• kharchenkolab/numbat

  Haplotype-aware CNV analysis from single-cell RNA-seq

  Language:R163918323

• theislab/zellkonverter

  Conversion between scRNA-seq objects

  Language:R14659827

• neherlab/pan-genome-analysis

  Processing pipeline for pan-genome visulization and exploration

  Language:Python132145037

• basilkhuder/Seurat-to-RNA-Velocity

  A guide to using a Seurat object in conjunction with RNA Velocity

  13062327

• EIDOSLAB/torchstain

  Stain normalization tools for histological analysis and computational pathology

  Language:Python11152220

• Nesvilab/MSFragger

  Ultrafast, comprehensive peptide identification for mass spectrometry–based proteomics

  Language:HTML103132557

• 10XGenomics/subset-bam

  Language:Rust66131510

• brentp/tiwih

  simple bioinformatics command-line (t)ools (i) (w)ished (i) (h)ad.

  Language:Nim44310

• estebanpw/chromeister

  A dotplot generator for large chromosomes

  Language:C394214

• bpucker/MGSE

  Mapping-based Genome Size Estimation (MGSE) performs an estimation of a genome size based on a read mapping to an existing genome sequence assembly.

  Language:Python31323

• djwooten/synergy

  Python library for calculting synergy of drug combinations using several drug synergy frameworks

  Language:Python279145

• cccnrc/plot-VCF

  visual analysis of your VCF files

  Language:R25193

• dcgerard/updog

  Flexible Genotyping of Polyploids using Next Generation Sequencing Data

  Language:R244278

• Sun-lab/ideas

  Individual level Differential Expression Analysis for Single cells

  Language:R22154

• bcgsc/PASS

  Proteome Assembler with Short peptide Sequence

  Language:Perl7512

• umich-brcf-bioinf/Jacquard

  Suite of command-line tools to expedite analysis of exome variant data from multiple patients and multiple variant callers.

  Language:Python7972

• jacob-sycoff/aml-white-blood-cell-classifier

  Uses deep learning to classify types of white blood cells in cell images from blood smear slides to aid in AML diagnosis.

  Language:Jupyter Notebook2201