huangnengCSU

huangnengCSU's Stars

• conda-forge/miniforge

  A conda-forge distribution.

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• snakemake/snakemake

  This is the development home of the workflow management system Snakemake. For general information, see

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• apptainer/apptainer

  Apptainer: Application containers for Linux

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• openwdl/wdl

  Workflow Description Language - Specification and Implementations

  78188304306

• pachterlab/kallisto

  Near-optimal RNA-Seq quantification

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• Illumina/SpliceAI

  A deep learning-based tool to identify splice variants

  Language:Python41221139161

• gpertea/gffread

  GFF/GTF utility providing format conversions, region filtering, FASTA sequence extraction and more

  Language:C++380913539

• davidaknowles/leafcutter

  Annotation-free quantification of RNA splicing. Yang I. Li, David A. Knowles, Jack Humphrey, Alvaro N. Barbeira, Scott P. Dickinson, Hae Kyung Im, Jonathan K. Pritchard

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• weberlab-hhu/Helixer

  Using Deep Learning to predict gene annotations

  Language:Python1731413329

• zengxiaofei/HapHiC

  HapHiC: a fast, reference-independent, allele-aware scaffolding tool based on Hi-C data

  Language:Python1444959

• epi2me-labs/wf-human-variation

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• htseq/htseq

  HTSeq is a Python library to facilitate processing and analysis of data from high-throughput sequencing (HTS) experiments.

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• nextflow-io/rnaseq-nf

  A proof of concept of RNAseq pipeline

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• gagneurlab/MMSplice_MTSplice

  Tissue-specific variant effect predictions on splicing

  Language:Jupyter Notebook4084521

• PacificBiosciences/paraphase

  HiFi-based caller for highly similar paralogous genes

  Language:Python367167

• brianli314/palindrome-finder

  A bioinformatics tool written in Rust to find palindromic sequences in DNA

  Language:Rust330

• nf-core/isoseq

  Genome annotation with PacBio Iso-Seq. Takes raw subreads as input, generate Full Length Non Chemiric (FLNC) sequences and produce a bed annotation.

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• LappalainenLab/lorals_paper_code

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• mktle/colorSV

  somatic SV calling on matched tumor-normal co-assembly graphs

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• guigolab/sQTLseekeR2

  R package to detect splicing QTLs (sQTLs)

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• CCICB/SpliceVarDB

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• chaolinzhanglab/DeltaSplice

  A neural network model to predict splice site usage and splicing-altering mutations

  Language:Python8211

• BovReg/BovReg_eQTL

  Repository

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• gxiaolab/isoLASER

  Language:Python70

• jolespin/pyhmmsearch

  Fast implementation of HMMSEARCH optimized for high-memory systems using PyHmmer

  Language:Python7110

• huangnengCSU/longcallR-nn

  longcallR_nn is a variant caller specifically designed for long-read RNA-seq data, utilizing a ResNet50 model.

  Language:Rust4100

• haydenji0731/transigner

  Language:Python3300

• huangnengCSU/longcallR-nf

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• huangnengCSU/variant_detection_nf

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• lyj95618/lorals

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