94 Open source projects that are alternatives of or similar to PECA

CWL tools and workflows for GGR

chromatin Variability Across Regions (of the genome!)

A comprehensive tool for processing, analyzing and visulizing single cell chromatin accessibility sequencing data

Fast visualization tool for large-scale and high dimensional single-cell data

Community-curated list of software packages and data resources for single-cell, including RNA-seq, ATAC-seq, etc.

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

Differential Gene Correlation Analysis

Multi-omics analysis protocols by Lyu.

Regulatory Genomics Toolbox: Python library and set of tools for the integrative analysis of high throughput regulatory genomics data.

GREIN : GEO RNA-seq Experiments Interactive Navigator

Haystack: Epigenetic Variability and Transcription Factor Motifs Analysis Pipeline

Single cell analysis in the browser

🐛 How to use CENTIPEDE to determine if a transcription factor is bound.

CellNet: network biology applied to stem cell engineering

RNASeq pipeline

AnaLysis routines for ePigenomicS data - 🏫 Bioconductor project

📊 Graphical User Interface for TCC package

Dynamical systems methods for RNA velocity analysis

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

This repository contains the tensorflow implementation of "GNE: A deep learning framework for gene network inference by aggregating biological information"

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

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

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

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

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

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

Streamlining SLAM-seq analysis with ultra-high sensitivity

R package to access DoRothEA's regulons

A versatile sequenced read processor for nanopore direct RNA sequencing

FEELnc : FlExible Extraction of LncRNA

Analysing Capture Seq Count Data

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

An automated RNA-seq pipeline using Nextflow

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

netZooM is a network biology package implemented in MATLAB.

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

Version 2.1.0 released

Porting DESeq2 and DEXSeq into python via rpy2

Feature extraction algorithm for genomic data

Deep Learning based cell composition analysis with Scaden.

Pipeline for annotating genomes using long read transcriptomics data with pinfish

Scripts to import your FeatureCounts output into DEXSeq

Next-Gen Sequencing tools from the Horvath Lab

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

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

Transcription factor Occupancy prediction By Investigation of ATAC-seq Signal

Interactive Differential Expression AnaLysis - DE made accessible and reproducible

Fast and accurate gene fusion detection from RNA-Seq data

CICERO: a versatile method for detecting complex and diverse driver fusions using cancer RNA sequencing data.

Fast in-silico normalization algorithm for NGS data

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

TCGA data acquisition and processing for Project Cognoma

RNA-seq analysis pipeline for detection gene-fusions

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

Spatial alignment of single cell transcriptomic data.

Summer school course materials collection

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

Reference-based transcript discovery from long RNA read

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

A proof of concept RNA-Seq pipeline with Nextflow