transcriptome

There are 98 repositories under transcriptome topic.

  • COMBINE-lab/salmon

    🐟 🍣 🍱 Highly-accurate & wicked fast transcript-level quantification from RNA-seq reads using selective alignment

    Language:C++78038839164

  • bcgsc/NanoSim

    Nanopore sequence read simulator

    Language:Python2471817958

  • ZJUFanLab/scCATCH

    Automatic Annotation on Cell Types of Clusters from Single-Cell RNA Sequencing Data

    Language:R22056538

  • mortazavilab/TALON

    Technology agnostic long read analysis pipeline for transcriptomes

    Language:Python137614630

  • greenelab/pancancer

    Building classifiers using cancer transcriptomes across 33 different cancer-types

    Language:Jupyter Notebook120102057

  • eead-csic-compbio/get_homologues

    GET_HOMOLOGUES: a versatile software package for pan-genome analysis

    Language:Perl1101711726

  • jminnier/STARTapp

    The START App: R Shiny Transcriptome Analysis Resource Tool

    Language:HTML9071441

  • federicomarini/GeneTonic

    Enjoy your transcriptomic data and analysis responsibly - like sipping a cocktail

    Language:R766258

  • bcgsc/mavis

    Merging, Annotation, Validation, and Illustration of Structural variants

    Language:Python741416214

  • comprna/RATTLE

    Reference-free reconstruction and error correction of transcriptomes from Nanopore long-read sequencing

    Language:C++5795510
  • swan_vis

    mortazavilab/swan_vis

    A Python library to visualize and analyze long-read transcriptomes

    Language:Jupyter Notebook5742311

  • federicomarini/pcaExplorer

    pcaExplorer - Interactive exploration of Principal Components of Samples and Genes in RNA-seq data

    Language:R56122117

  • ksahlin/isONclust

    De novo clustering of long transcript reads into genes

    Language:Python505248

  • enormandeau/gawn

    Genome Annotation Without Nightmares

    Language:Perl4321313

  • drostlab/myTAI

    Evolutionary Transcriptomics with R

    Language:R4161718

  • bcgsc/transabyss

    de novo assembly of RNA-seq data using ABySS

    Language:Python34202914

  • nf-core/lncpipe

    UNDER DEVELOPMENT--- Analysis of long non-coding RNAs from RNA-seq datasets

    Language:Nextflow34191117

  • cfarkas/annotate_my_genomes

    A genome annotation pipeline that use short and long sequencing reads alignments from animal genomes

    Language:Nextflow29233

  • fairliereese/LR-splitpipe

    Demultiplexing and debarcoding tool designed for LR-Split-seq data.

    Language:Python201104

  • hyeshik/tailseeker

    Software for measuring poly(A) tail length and 3′-end modifications using a high-throughput sequencer

    Language:C197157

  • svm-zhang/AGOUTI

    Annotated Genome Optimization Using Transcriptome Information

    Language:Python193188

  • hr1912/TreeExp

    TreeExp 2.0: Toolbox for analyzing expression evolution based on RNA-seq count data

    Language:R15314

  • ksahlin/IsoCon

    Derives consensus sequences from a set of long noisy reads by clustering and error correction.

    Language:Python15591

  • guigolab/tmerge

    Merge transcriptome read-to-genome alignments into non-redundant transcript models

    Language:Perl13213

  • jaleesr/TrendCatcher

    TrendCatcher is an open source R-package that allows users to systematically analyze and visualize time course data. Please cite "Temporal transcriptomic analysis using TrendCatcher identifies early and persistent neutrophil activation in severe COVID-19" by Xinge Wang et al published in JCI Insight (2022) - https://insight.jci.org/articles/view/157255

    Language:R112123

  • jingwyang/AnceTran

    AnceTran2.0: R package for transcriptome evolution analysis based on RNA-seq expression data or ChIP-seq TF-binding data

    Language:R11230

  • tjiagoM/gtex-transcriptome-modelling

    Multilayer modelling of the human transcriptome and biological mechanisms of complex diseases and traits

    Language:Jupyter Notebook11212

  • iyhaoo/DISC

    A highly scalable and accurate inference of gene expression and structure for single-cell transcriptomes using semi-supervised deep learning.

    Language:HTML10135

  • pblumenkamp/GenExVis

    An application for exploring and visualizing differential gene expression data created with DESeq2

    Language:Vue102880

  • nf-core/denovotranscript

    A pipeline for de novo transcriptome assembly of paired-end short reads from bulk RNA-seq

    Language:Nextflow918713

  • xie-lab/DISC

    A highly scalable and accurate inference of gene expression and structure for single-cell transcriptomes using semi-supervised deep learning.

    Language:HTML9103

  • charles-plessy/tutorial

    Various tutorials on how to analyse transcriptomic data.

    Language:HTML8201

  • jlanga/smsk_trinotate

    Snakemake workflow to run transdecoder + trinotate

    Language:Python8482

  • segalmicrobiomelab/lung_cancer_microbiome

    Language:R8202

  • UrszulaCzerwinska/DeconICA

    Deconvolution of transcriptome through Immune Component Analysis

    Language:MATLAB83175

  • nf-core/hicar

    Pipeline for HiCAR data, a robust and sensitive multi-omic co-assay for simultaneous measurement of transcriptome, chromatin accessibility and cis-regulatory chromatin contacts.

    Language:Nextflow78585