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Top 24 transcriptomics open source projects

Method for Identifying Novel Transcripts and Isoforms using Equivalence classes, in cancer and rare disease.

✭ 24

python groovy shell r rna-seq cancer transcriptomics structural-variation duplications rare-disease gene-fusions cryptic-variants

bacnet

BACNET is a Java based platform to develop website for multi-omics analysis

✭ 12

java website bioinformatics genomics data-visualization proteomics transcriptomics bacnet multi-omics listeria

cell-ontology

An ontology of cell types

✭ 75

Makefile common lisp perl shell scala ruby genomics semantic-web owl ontology transcriptomics anatomy metazoa obofoundry cell-ontology cell-types anatomy-ontology

EWCE

Expression Weighted Celltype Enrichment. See the package website for up-to-date instructions on usage.

✭ 30

r Dockerfile TeX transcriptomics single-cell deconvolution single-cell-rna-seq

alevin-fry

🐟 🔬🦀 alevin-fry is an efficient and flexible tool for processing single-cell sequencing data, currently focused on single-cell transcriptomics and feature barcoding.

✭ 78

rust shell rna-seq quantification transcriptomics single-cell 10x single-cell-rna-seq

MetaOmGraph

MetaOmGraph: a workbench for interactive exploratory data analysis of large expression datasets

✭ 30

java Makefile bioinformatics rna-seq exploratory-data-analysis transcriptomics mog cancer-data big-data-visualization

DigitalCellSorter

Digital Cell Sorter (DCS): single cell RNA-seq analysis toolkit. Documentation:

✭ 19

python Batchfile visualization quality-control gene clustering identification transcriptomics anomaly-detection batch-correction single-cell-sequencing-analysis automatic-cell-identification cancer-heterogeneity

IsoQuant

Reference-based transcript discovery from long RNA read

✭ 26

python bioinformatics rna-seq nanopore ngs pacbio transcriptomics

DEcode

A prediction model for differential gene expression (DE) based on genome-wide regulatory interactions

✭ 16

Jupyter Notebook python r bioinformatics deep-neural-networks systems-biology computational-biology transcriptomics

dammit

just annotate it, dammit!

✭ 82

python Jupyter Notebook bioinformatics annotation transcriptomics

paccmann rl

Code pipeline for the PaccMann^RL in iScience: https://www.cell.com/iscience/fulltext/S2589-0042(21)00237-6

✭ 22

deep-learning drug-discovery transcriptomics generative-models drug-sensitivity de-novo-drug-design

Pando

Multiome GRN inference.

✭ 21

r transcriptomics single-cell epigenomics

TransPi

TransPi – a comprehensive TRanscriptome ANalysiS PIpeline for de novo transcriptome assembly

✭ 18

Nextflow shell r python Dockerfile rna-seq annotation transcriptomics denovo-assembly rna-seq-pipeline nextflow-pipeline non-model-species

dee2

Digital Expression Explorer 2 (DEE2): a repository of uniformly processed RNA-seq data

✭ 32

shell HTML r Dockerfile data-mining bioinformatics rna-seq genomics genetics transcriptomics rna-expression

pisces

PISCES is a pipeline for rapid transcript quantitation, genetic fingerprinting, and quality control assessment of RNAseq libraries using Salmon.

✭ 23

python r TeX bioinformatics bioinformatics-pipeline rnaseq transcriptomics salmon rnaseq-pipeline

GeneTonic

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

✭ 66

r gui shiny reproducible-research gene-expression data-visualization bioconductor transcriptome user-friendly data-exploration transcriptomics rna-seq-analysis pathway-analysis rna-seq-data bioconductor-package functional-enrichment-analysis

pychopper

A tool to identify, orient, trim and rescue full length cDNA reads

✭ 74

python Makefile shell rna-seq nanopore transcriptomics cdna full-length

scCATCH

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

✭ 137

r rna-seq sequencing transcriptome transcriptomics single-cell marker-genes seurat cluster-annotation cell-markers

MERlin

MERlin is an extensible analysis pipeline applied to decoding MERFISH data

✭ 19

python modular image-processing pipeline-framework cloud-computing segmentation transcriptomics merfish

diffxpy

Differential expression analysis for single-cell RNA-seq data.

✭ 137

python bioinformatics tensorflow transcriptomics gene-set-enrichment differential-expression single-cell-rna-seq

pipeline-pinfish-analysis

Pipeline for annotating genomes using long read transcriptomics data with pinfish

✭ 27

python rna-seq nanopore genome-annotation transcriptomics cdna

scrattch.vis

scRNA-seq data visualization from scrattch

✭ 18

r data-visualization transcriptomics scrattch

cosmosR

COSMOS (Causal Oriented Search of Multi-Omic Space) is a method that integrates phosphoproteomics, transcriptomics, and metabolomics data sets.

✭ 30

r CSS data-integration proteomics phosphoproteomics transcriptomics network-modelling metabolomic-data

bioc 2020 tidytranscriptomics

Workshop on tidytranscriptomics: Performing tidy transcriptomics analyses with tidybulk, tidyverse and tidyheatmap

✭ 25

r Dockerfile workshop heatmap tidy-data tidyverse pca bioconductor mds transcriptomics differential-expression tidybulk bioc2020

1-24 of 24 transcriptomics projects