60 Open source projects that are alternatives of or similar to CICERO

A course on Analysing Next Generation (/High Throughput etc..) Sequencing data using Bioconductor

CellO: Gene expression-based hierarchical cell type classification using the Cell Ontology

PECA is a software for inferring context specific gene regulatory network from paired gene expression and chromatin accessibility data

An automated RNA-seq pipeline using Nextflow

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

Pipeline to find aberrant events in RNA-Seq data, useful for diagnosis of rare disorders

Accord Project Documentation

Automated generation of tailored bioinformatics Jupyter Notebooks via a user interface.

Version 2.1.0 released

Differential Gene Correlation Analysis

A Snakemake workflow for differential expression analysis of RNA-seq data with Kallisto and Sleuth.

Interactive Differential Expression AnaLysis - DE made accessible and reproducible

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

Multi-omics analysis protocols by Lyu.

A pipeline for the computational evaluation of RNA-Seq data

Fast in-silico normalization algorithm for NGS data

GREIN : GEO RNA-seq Experiments Interactive Navigator

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

Differential expression (DE); gene set Enrichment Analysis (GSEA); single cell RNAseq studies (scRNAseq)

🚦 Run Picard on BAM files and collate 90 metrics into one file.

Pipeline for annotating genomes using long read transcriptomics data with pinfish

Feature extraction algorithm for genomic data

🐍 Snakefiles for common RNA-seq data analysis workflows.

Reproducible bioinformatics pipelines in python. Import any Unix tool/command in python.

A graphical user interface for distributed data processing of high throughput genomics

Scripts to import your FeatureCounts output into DEXSeq

FEELnc : FlExible Extraction of LncRNA

CWL tools and workflows for GGR

Single cell analysis in the browser

Reference-based transcript discovery from long RNA read

📊 Graphical User Interface for TCC package

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

Deep Learning based cell composition analysis with Scaden.

RNA-seq analysis pipeline for detection gene-fusions

A versatile sequenced read processor for nanopore direct RNA sequencing

Lightweight and Fast; RNA-seq quantification at the event-level

Next-Gen Sequencing tools from the Horvath Lab

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

CellNet: network biology applied to stem cell engineering

kallisto | bustools workflow for pre-processing single-cell RNA-seq data

RNASeq pipeline

Reproducible reanalysis of a combined ChIP-Seq & RNA-Seq data set

Dynamical systems methods for RNA velocity analysis

Haystack: Epigenetic Variability and Transcription Factor Motifs Analysis Pipeline

Pileup biallelic SNPs from single-cell and bulk RNA-seq data

An online companion to the OSCA manuscript demonstrating Bioconductor resources and workflows for single-cell RNA-seq analysis.

CoNekT (short for Co-expression Network Toolkit) is a platform to browse co-expression data and enable cross-species comparisons.

Processing of single cell RNAseq data for the recovery of TCRs in python

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

Summer school course materials collection

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

A proof of concept RNA-Seq pipeline with Nextflow

Streamlining SLAM-seq analysis with ultra-high sensitivity

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

Create a cromphensive report of DEG list coming from any analysis of RNAseq data

Porting DESeq2 and DEXSeq into python via rpy2

SQUID detects both fusion-gene and non-fusion-gene structural variations from RNA-seq data

Nextflow RNA-Seq Best Practice analysis pipeline, used at the SciLifeLab National Genomics Infrastructure.

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

Fast and accurate gene fusion detection from RNA-Seq data