transcriptome

There are 3 repositories under transcriptome topic.

COMBINE-lab / salmon
🐟 🍣 🍱 Highly-accurate & wicked fast transcript-level quantification from RNA-seq reads using selective alignment
quasi-mapping bioinformatics rna-seq rnaseq salmon quantification sailfish c-plus-plus gene-expression scrna-seq single-cell 10x selective-alignment rna-seq-quantification single-cell-rna-seq transcriptome
Language:C++ 727
bcgsc / NanoSim
Nanopore sequence read simulator
genome transcriptome simulator oxford-nanopore nanopore-sequencing
Language:Python 213
ZJUFanLab / scCATCH
Automatic Annotation on Cell Types of Clusters from Single-Cell RNA Sequencing Data
marker-genes cell-markers cluster-annotation seurat single-cell rna-seq transcriptomics sequencing transcriptome
Language:R 202
mortazavilab / TALON
Technology agnostic long read analysis pipeline for transcriptomes
oxford-nanopore pacbio transcript-quantification transcriptome
Language:Python 126
greenelab / pancancer
Building classifiers using cancer transcriptomes across 33 different cancer-types
tcga classifier transcriptome pancancer cancer gene-expression machine-learning methodology tool analysis
Language:Jupyter Notebook 118
eead-csic-compbio / get_homologues
GET_HOMOLOGUES: a versatile software package for pan-genome analysis
pangenome bacteria annotation plants transcriptome clustering fasta genbank pangene
Language:Perl 99
jminnier / STARTapp
The START App: R Shiny Transcriptome Analysis Resource Tool
shiny-apps shiny rna-seq transcriptome visualization r genome-biology bioinformatics
Language:HTML 86
federicomarini / GeneTonic
Enjoy your transcriptomic data and analysis responsibly - like sipping a cocktail
rna-seq-data rna-seq-analysis transcriptomics r shiny transcriptome reproducible-research gui user-friendly bioconductor bioconductor-package functional-enrichment-analysis pathway-analysis gene-expression data-visualization data-exploration
Language:R 75
bcgsc / mavis
Merging, Annotation, Validation, and Illustration of Structural variants
genomics visualization python structural-variation bioinformatics transcriptome
Language:Python 68
comprna / RATTLE
Reference-free reconstruction and error correction of transcriptomes from Nanopore long-read sequencing
clustering nanopore transcriptome bioinformatics rna-seq genomics
Language:C++ 54
federicomarini / pcaExplorer
pcaExplorer - Interactive exploration of Principal Components of Samples and Genes in RNA-seq data
principal-components rna-seq-data rna-seq-analysis r shiny transcriptome reproducible-research user-friendly bioconductor
Language:R 52
swan_vis
mortazavilab / swan_vis
A Python library to visualize and analyze long-read transcriptomes
bioinformatics long-read oxford-nanopore pacbio pacbio-iso-seq transcriptome
Language:Jupyter Notebook 48
ksahlin / isONclust
De novo clustering of long transcript reads into genes
bioinformatics clustering oxford-nanopore pacbio-iso-seq transcriptome
Language:Python 42
enormandeau / gawn
Genome Annotation Without Nightmares
genome-annotation transcriptome pipeline genomics
Language:Perl 39
drostlab / myTAI
Evolutionary Transcriptomics with R
evolutionary-transcriptomics r transcriptome evolution evo-devo studies-transcriptomes biological-processes gene-sets mytai gene-expression conservation expression-profiles
Language:R 35
bcgsc / transabyss
de novo assembly of RNA-seq data using ABySS
bioinformatics rna-seq transcriptome transcriptome-assembly
Language:Python 33
nf-core / lncpipe
UNDER DEVELOPMENT--- Analysis of long non-coding RNAs from RNA-seq datasets
lncrna rna-seq-analysis transcriptome differential-expression nf-core nextflow workflow pipeline rna long-non-coding non-coding
Language:Nextflow 30
cfarkas / annotate_my_genomes
A genome annotation pipeline that use short and long sequencing reads alignments from animal genomes
transcriptome-assembly transcriptome genome-annotation rna-seq stringtie braker2
Language:Nextflow 22
hyeshik / tailseeker
Software for measuring poly(A) tail length and 3′-end modifications using a high-throughput sequencer
transcriptome rna-seq snakemake molecular-biology mrna polya-tail pipeline
Language:C 18
fairliereese / LR-splitpipe
Demultiplexing and debarcoding tool designed for LR-Split-seq data.
single-cell long-read transcriptome rna-seq demultiplexing
Language:Python 16
hr1912 / TreeExp
TreeExp 2.0: Toolbox for analyzing expression evolution based on RNA-seq count data
expression-character-tree expression-evolution transcriptome
Language:R 15
ksahlin / IsoCon
Derives consensus sequences from a set of long noisy reads by clustering and error correction.
ccs clustering transcriptome error-correction long-reads bioinformatics
Language:Python 13
jingwyang / AnceTran
AnceTran2.0: R package for transcriptome evolution analysis based on RNA-seq expression data or ChIP-seq TF-binding data
transcriptome distance-estimation character-tree-building ancestral-inference rna-seq chip-seq
Language:R 11
guigolab / tmerge
Merge transcriptome read-to-genome alignments into non-redundant transcript models
bioinformatics genome genomics long-read merge sequencing transcriptome transcriptomics
Language:Perl 10
iyhaoo / DISC
A highly scalable and accurate inference of gene expression and structure for single-cell transcriptomes using semi-supervised deep learning.
single-cell transcriptome deep-learning semi-supervised-learning imputation
Language:HTML 10
tjiagoM / gtex-transcriptome-modelling
Multilayer modelling of the human transcriptome and biological mechanisms of complex diseases and traits
paper gtex transcriptome tcga ukbiobank multilayer-network vae python umap twas
Language:Jupyter Notebook 10
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
rna-seq transcriptomics transcriptome temporal-data visualization r single-cell
Language:R 9
xie-lab / DISC
A highly scalable and accurate inference of gene expression and structure for single-cell transcriptomes using semi-supervised deep learning.
single-cell transcriptome deep-learning semi-supervised-learning imputation
Language:HTML 9
charles-plessy / tutorial
Various tutorials on how to analyse transcriptomic data.
cage transcriptome fantom tutorial edger
Language:HTML 8
jlanga / smsk_trinotate
Snakemake workflow to run transdecoder + trinotate
transcriptome snakemake snakemake-workflows trinity transdecoder trinotate blast hmmscan sqlite
Language:Python 8
pblumenkamp / GenExVis
An application for exploring and visualizing differential gene expression data created with DESeq2
deseq2 deseq2-analysis differential-expression differential-gene-expression rna-seq transcriptomics transcriptome visualization
Language:Vue 8
segalmicrobiomelab / lung_cancer_microbiome
microbiome multiomics transcriptome 16s-rrna 16s rna-seq rna-seq-analysis
Language:R 8
UrszulaCzerwinska / DeconICA
Deconvolution of transcriptome through Immune Component Analysis
deconvolution transcriptome biology signal-processing
Language:MATLAB 8
xiangyue9607 / single-cell-classification
We use two kinds of neural networks: Multilayer Perceptron (MLP) and Recurrent Neural Network (RNN) to predict the single-cell cycle stage based on transcriptome data.
neural-network transcriptome
Language:Python 7
EBI-Metagenomics / workflow-is-cwl
This repository contains CWL descriptions of the various tools which will allow you to build workflows for the annotation of transcripts
common-workflow-language cwl cwl-description cwl-descriptions cwl-workflow diamond marine phmmer transcriptome transdecoder workflow
Language:HTML 6
kullrich / orthomap
orthomap is a python package to extract orthologous maps (in other words the evolutionary age of a given orthologous group) from OrthoFinder/eggNOG results. Orthomap results (gene ages per orthogroup) can be further used to calculate weigthed expression data (transcriptome evolutionary index) from scRNA sequencing objects.
orthofinder phylostratigraphy scanpy scrna-seq-analysis evolution expression-profiles gene-expression gene-expression-profiles bioinformatics orthomap python tai transcriptome
Language:Python 6

transcriptome

COMBINE-lab / salmon

bcgsc / NanoSim

ZJUFanLab / scCATCH

mortazavilab / TALON

greenelab / pancancer

eead-csic-compbio / get_homologues

jminnier / STARTapp

federicomarini / GeneTonic

bcgsc / mavis

comprna / RATTLE

federicomarini / pcaExplorer

mortazavilab / swan_vis

ksahlin / isONclust

enormandeau / gawn

drostlab / myTAI

bcgsc / transabyss

nf-core / lncpipe

cfarkas / annotate_my_genomes

hyeshik / tailseeker

fairliereese / LR-splitpipe

hr1912 / TreeExp

ksahlin / IsoCon

jingwyang / AnceTran

guigolab / tmerge

iyhaoo / DISC

tjiagoM / gtex-transcriptome-modelling

jaleesr / TrendCatcher

xie-lab / DISC

charles-plessy / tutorial

jlanga / smsk_trinotate

pblumenkamp / GenExVis

segalmicrobiomelab / lung_cancer_microbiome

UrszulaCzerwinska / DeconICA

xiangyue9607 / single-cell-classification

EBI-Metagenomics / workflow-is-cwl

kullrich / orthomap