Alternatives and similar repositories for cyclone

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

• HumanCellAtlas / skylab
  Soon to be deprecated in favor of broadinstitute/warp github repo. Previously: Secondary analysis pipelines
  ☆48Updated 7 months ago
• YosefLab / scone
  ☆55Updated 8 months ago
• rhondabacher / SCnorm
  Normalization for single cell RNA-seq data
  ☆49Updated 4 months ago
• pachterlab / scRNA-Seq-TCC-prep
  Preprocessing of single-cell RNA-Seq (deprecated)
  ☆62Updated 6 years ago
• kdkorthauer / scDD
  R package to identify genes with differential distributions in single-cell RNA-seq
  ☆33Updated 3 years ago
• markrobinsonuzh / conquer
  consistent quantification of external RNA-seq data sets
  ☆58Updated last year
• govinda-kamath / clustering_on_transcript_compatibility_counts
  Clustering cells from single cell RNA seq assays
  ☆46Updated 6 years ago
• kkdey / CountClust
  A R package for Grade of Membership model and Visualization of counts data:
  ☆32Updated 4 years ago
• JEFworks / liger
  Lightweight Iterative Gene set Enrichment in R
  ☆57Updated last year
• pachterlab / NYMP_2018
  ☆28Updated 6 years ago
• jessemzhang / tn_test
  post-clustering differential expression test
  ☆36Updated 6 years ago
• montilab / hypeR
  An R Package for Geneset Enrichment Workflows
  ☆76Updated last month
• Neurosurgery-Brain-Tumor-Center-DiazLab / scell
  Single-CELL rna-seq analysis software
  ☆39Updated 8 years ago
• mojaveazure / loomR
  An R-based interface for loom files
  ☆67Updated 5 years ago
• MSingerLab / COMETSC
  COMET Single-Cell Marker Detection tool
  ☆31Updated 3 years ago
• davismcc / archive-scater
  An archived version of the scater repository, see https://github.com/davismcc/scater for the active version.
  ☆64Updated 8 years ago
• bvieth / scRNA-seq-pipelines
  Compendium to "A Systematic Evaluation of Single Cell RNA-Seq Analysis Pipelines"
  ☆55Updated 4 years ago
• pachterlab / sircel
  Identify cell barcodes from single-cell genomics sequencing experiments
  ☆43Updated 3 years ago
• WeiqiangZhou / BIRD
  Big data Regression for predicting DNase I hypersensitivity
  ☆31Updated last year
• rajanil / msCentipede
  A hierarchical multiscale model for inferring transcription factor binding from chromatin accessibility data.
  ☆26Updated 9 years ago
• slowkow / tftargets
  Human transcription factor target genes from 6 databases in convenient R format.
  ☆86Updated 7 years ago
• vanheeringen-lab / scepia
  Single Cell Epigenome-based Inference of Activity
  ☆19Updated 2 years ago
• czi-hca-comp-tools / easy-data
  easy access to benchmark datasets
  ☆50Updated 7 years ago
• caleblareau / gchromVAR
  Cell type specific enrichments using finemapped variants and quantitative epigenetic data
  ☆45Updated 2 years ago
• dgrun / RaceID
  Algorithm for the inference of cell types from single-cell RNA-seq data.
  ☆45Updated 9 years ago
• pachterlab / kallisto-transcriptome-indices
  Reference transcriptome indices build from kallisto for popular organisms
  ☆44Updated last year
• waldronlab / HGNChelper
  Identify and correct invalid gene symbols
  ☆59Updated 11 months ago
• lanagarmire / SSrGE
  ☆34Updated 6 years ago
• sandhya212 / BISCUIT_SingleCell_IMM_ICML_2016
  R Codebase for BISCUIT: Infinite Mixture Model to cluster and impute single cells.
  ☆66Updated 7 years ago
• lilab-bcb / cumulus
  Cloud-based scalable and efficient single-cell genomics workflows
  ☆67Updated this week