Alternatives and similar repositories for GENIE3

Users that are interested in GENIE3 are comparing it to the libraries listed below

• broadinstitute / single_cell_classification
  Methods to use SNPs or gene expression to classify single cell RNAseq to reference profiles
  ☆30Updated 5 years ago
• GreenleafLab / motifmatchr
  Fast motif matching in R
  ☆46Updated last year
• juliaolivieri / SpliZ_pipeline
  Code to calculate the Splicing Z Score (SpliZ) for single cell RNA-seq splicing analysis
  ☆35Updated 4 years ago
• GreenleafLab / chromVARmotifs
  R package with motifs for use with chromVAR
  ☆28Updated 8 years ago
• tianshilu / QBRC-Neoantigen-Pipeline
  QBRC Neoantigen calling pipeline with CSiN calculation embedded
  ☆25Updated 3 years ago
• friedue / course_RNA-seq2019
  ☆36Updated 3 years ago
• salzman-lab / SICILIAN
  ☆23Updated last year
• gandallab / Dev_Brain_IsoSeq
  Bulk (CP/GZ) and single-cell Iso-Seq in the developing human brain
  ☆15Updated last year
• fmicompbio / monaLisa
  binned motif enrichment analysis and visualisation
  ☆44Updated 2 months ago
• Sun-lab / ideas
  Individual level Differential Expression Analysis for Single cells
  ☆26Updated 3 years ago
• dan-landau / IronThrone-GoT
  processes GoT amplicon data and generates a table of metrics
  ☆32Updated 3 years ago
• YeoLab / rbp-maps
  splicing and feature maps for RBPs
  ☆25Updated 3 years ago
• KCCG / rageseq
  RAGE-seq scripts
  ☆18Updated 4 years ago
• minoda-lab / universc
  UniverSC: a flexible cross-platform single-cell data processing pipeline
  ☆46Updated last year
• r3fang / snATAC
  <<------ Use SnapATAC!!
  ☆26Updated 6 years ago
• rargelaguet / scnmt_gastrulation
  scNMT-seq gastrulation
  ☆42Updated 2 years ago
• CFeregrino / scWGCNA
  scWGCNA
  ☆61Updated 3 years ago
• lanagarmire / SSrGE
  ☆34Updated 6 years ago
• cole-trapnell-lab / cicero-release
  ☆59Updated last year
• nf-core / scflow
  Please consider using/contributing to https://github.com/nf-core/scdownstream
  ☆26Updated last year
• songw01 / MEGENA
  Multiscale embedded gene co-expression network analysis
  ☆57Updated 2 years ago
• cboix / EPIMAP_ANALYSIS
  Epimap processing and analysis code repository
  ☆33Updated 3 years ago
• wuaipinglab / ImmuCC
  Cell-Centric View of Tissue Transcriptome Measuring Cellular Compositions of Immune Microenvironment From Mouse RNA-Seq Data.
  ☆26Updated 4 years ago
• TheJacksonLaboratory / BRCA-LRseq-pipeline
  Pipeline to analyze long-read mRNA isoforms and ORF products sequenced in breast cancer using PacBio Single-Molecule technology.
  ☆16Updated 3 years ago
• neurorestore / DE-analysis
  ☆39Updated 4 years ago
• Xinglab / PEGASAS
  Pathway Enrichment-Guided Activity Study of Alternative Splicing (PEGASAS)
  ☆20Updated 3 years ago
• McGranahanLab / TcellExTRECT
  ☆48Updated last year
• frattalab / splicing
  Snakemake pipeline for running MAJIQ
  ☆23Updated 2 years ago
• wenweixiong / MARVEL
  ☆53Updated last year
• combiz / scFlow
  Single-cell/nuclei RNA-seq analysis tools in R for a complete workflow.
  ☆57Updated last year