Alternatives and similar repositories for SCITE

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

• mahmoudibrahim / JAMM
  JAMM Peak Finder for Sequencing Datasets
  ☆29Updated 5 years ago
• JEFworks / liger
  Lightweight Iterative Gene set Enrichment in R
  ☆57Updated last year
• pachterlab / sircel
  Identify cell barcodes from single-cell genomics sequencing experiments
  ☆43Updated 3 years ago
• SamBuckberry / RUN-WGCNA
  Wrapper R scripts for performing a weighted-gene co-expression network analysis (WGCNA)
  ☆29Updated 10 years ago
• yuchaojiang / Canopy
  Accessing Intra-Tumor Heterogeneity and Tracking Longitudinal and Spatial Clonal Evolutionary History by Next-Generation Sequencing.
  ☆70Updated 4 years ago
• yuchaojiang / SCALE
  Allele-Specific Expression by Single-Cell RNA Sequencing
  ☆29Updated 5 years ago
• gtrichard / deepStats
  deepStats: a stastitical toolbox for deeptools and genomic signals
  ☆35Updated 4 years ago
• Dowell-Lab / DAStk
  Differential ATAC-seq toolkit
  ☆27Updated last year
• rajanil / msCentipede
  A hierarchical multiscale model for inferring transcription factor binding from chromatin accessibility data.
  ☆26Updated 9 years ago
• jw156605 / SingleSplice
  Algorithm for detecting alternative splicing in a population of single cells. See details in Welch et al., Nucleic Acids Research 2016: h…
  ☆22Updated 9 years ago
• cfce / chilin
  ChIP-seq DC and QC Pipeline
  ☆36Updated 4 years ago
• YeoLab / outrigger
  Create a *de novo* alternative splicing database, validate splicing events, and quantify percent spliced-in (Psi) from RNA seq data
  ☆67Updated 5 years ago
• daler / chromhmm-tools
  Helpers for working with ChromHMM (http://compbio.mit.edu/ChromHMM/)
  ☆17Updated 7 years ago
• shawnzhangyx / PePr
  a peak-calling and differential analysis tool for replicated ChIP-Seq data
  ☆36Updated 3 years ago
• GarrettJenkinson / informME
  An information-theoretic pipeline for methylation analysis of WGBS data
  ☆24Updated 6 years ago
• hms-dbmi / spp
  SPP - R package for analysis of ChIP-seq and other functional sequencing data
  ☆43Updated 4 years ago
• pachterlab / scRNA-Seq-TCC-prep
  Preprocessing of single-cell RNA-Seq (deprecated)
  ☆62Updated 6 years ago
• rhondabacher / SCnorm
  Normalization for single cell RNA-seq data
  ☆49Updated 4 months ago
• HumanCellAtlas / skylab
  Soon to be deprecated in favor of broadinstitute/warp github repo. Previously: Secondary analysis pipelines
  ☆48Updated 7 months ago
• dan-landau / IronThrone-GoT
  processes GoT amplicon data and generates a table of metrics
  ☆32Updated 3 years ago
• UMMS-Biocore / debrowser
  Differential Count Data Analysis Toolbox
  ☆61Updated last year
• reiterlab / treeomics
  Decrypting somatic mutation patterns to reveal the evolution of cancer
  ☆56Updated 4 years ago
• nellore / intropolis
  Exon-exon splice junctions across SRA
  ☆42Updated 4 years ago
• Danko-Lab / rtfbs_db
  Parse TF motifs from public databases, read into R, and scan using 'rtfbs'.
  ☆23Updated 6 years ago
• thelovelab / tximeta
  Transcript quantification import with automatic metadata detection
  ☆67Updated 3 weeks ago
• pinellolab / haystack_bio
  Haystack: Epigenetic Variability and Transcription Factor Motifs Analysis Pipeline
  ☆47Updated 3 years ago
• caravagnalab / revolver
  Tumour stratification by maximum-likelihood repeated evolution from multi-region sequencing data
  ☆66Updated 2 years ago
• GreenleafLab / NucleoATACR
  R package for reading in & working with NucleoATAC outputs
  ☆26Updated 7 years ago
• slowkow / picardmetrics
  Run Picard on BAM files and collate 90 metrics into one file.
  ☆40Updated 8 years ago
• FunGeST / Palimpsest
  An R package for studying mutational signatures and structural variant signatures along clonal evolution in cancer.
  ☆71Updated last year