Ecosyste.ms: Packages
An open API service providing package, version and dependency metadata of many open source software ecosystems and registries.
bioconductor.org "Transcriptomics" keyword
brainflowprobes 1.18.0
Plots and annotation for choosing BrainFlow target probe sequence3 versions - Latest release: about 1 month ago - 5.01 thousand downloads total - 0 stars on GitHub - 1 maintainer
Top 4.0% on bioconductor.org
3 versions - Latest release: 25 days ago - 4 dependent packages - 77 thousand downloads total - 25 stars on GitHub - 1 maintainer
ALDEx2 1.36.0
Analysis Of Differential Abundance Taking Sample and Scale Variation Into Account3 versions - Latest release: 25 days ago - 4 dependent packages - 77 thousand downloads total - 25 stars on GitHub - 1 maintainer
cosmosR 1.12.0
COSMOS (Causal Oriented Search of Multi-Omic Space)3 versions - Latest release: 19 days ago - 3.99 thousand downloads total - 53 stars on GitHub - 1 maintainer
CuratedAtlasQueryR 1.2.0
Queries the Human Cell Atlas3 versions - Latest release: 27 days ago - 1.22 thousand downloads total - 77 stars on GitHub - 1 maintainer
GEOexplorer 1.10.0
GEOexplorer: a webserver for gene expression analysis and visualisation3 versions - Latest release: about 1 month ago - 3.04 thousand downloads total - 4 stars on GitHub - 1 maintainer
TREG 1.8.0
Tools for finding Total RNA Expression Genes in single nucleus RNA-seq data3 versions - Latest release: about 1 month ago - 2.03 thousand downloads total - 4 stars on GitHub - 1 maintainer
scBubbletree 1.6.0
Quantitative visual exploration of scRNA-seq data3 versions - Latest release: 25 days ago - 1.74 thousand downloads total - 4 stars on GitHub - 1 maintainer
Top 5.5% on bioconductor.org
3 versions - Latest release: about 1 month ago - 8 dependent packages - 34.1 thousand downloads total - 220 stars on GitHub - 1 maintainer
iSEE 2.16.0
Interactive SummarizedExperiment Explorer3 versions - Latest release: about 1 month ago - 8 dependent packages - 34.1 thousand downloads total - 220 stars on GitHub - 1 maintainer
HybridExpress 1.0.0
Comparative analysis of RNA-seq data for hybrids and their progenitors1 version - Latest release: about 1 month ago - 347 downloads total - 0 stars on GitHub - 1 maintainer
consICA 2.2.0
consensus Independent Component Analysis3 versions - Latest release: about 1 month ago - 2.58 thousand downloads total - 0 stars on GitHub - 1 maintainer
mosdef 1.0.0
MOSt frequently used and useful Differential Expression Functions1 version - Latest release: about 1 month ago - 0 stars on GitHub - 1 maintainer
SpotSweeper 0.99.5
Spatially-aware quality control for spatial transcriptomics2 versions - Latest release: about 1 month ago - 137 downloads total - 0 stars on GitHub - 1 maintainer
SingleCellAlleleExperiment 0.99.5
S4 Class for Single Cell Data with Allele and Functional Levels for Immune Genes2 versions - Latest release: about 1 month ago - 215 downloads total - 5 stars on GitHub - 1 maintainer
iSEEfier 1.0.0
Streamlining the creation of initial states for starting an iSEE instance1 version - Latest release: about 1 month ago - 295 downloads total - 0 stars on GitHub - 1 maintainer
tidyomics 0.99.7
Easily install and load the tidyomics ecosystem2 versions - Latest release: about 1 month ago - 366 downloads total - 18 stars on GitHub - 1 maintainer
spoon 0.99.10
Address the Mean-variance Relationship in Spatial Transcriptomics Data2 versions - Latest release: about 1 month ago - 292 downloads total - 0 stars on GitHub - 1 maintainer
tpSVG 0.99.7
Thin plate models to detect spatially variable genes2 versions - Latest release: about 1 month ago - 292 downloads total - 0 stars on GitHub - 1 maintainer
RIVER 1.26.0
R package for RIVER (RNA-Informed Variant Effect on Regulation)3 versions - Latest release: 7 months ago - 8.83 thousand downloads total - 10 stars on GitHub - 1 maintainer
ompBAM 1.6.0
C++ Library for OpenMP-based multi-threaded sequential profiling of Binary Alignment Map (BAM) files3 versions - Latest release: 7 months ago - 1 dependent package - 3.04 thousand downloads total - 2 stars on GitHub - 1 maintainer
Top 1.5% on bioconductor.org
4 versions - Latest release: about 1 month ago - 96 dependent packages - 625 thousand downloads total - 1 maintainer
scater 1.32.0
Single-Cell Analysis Toolkit for Gene Expression Data in R4 versions - Latest release: about 1 month ago - 96 dependent packages - 625 thousand downloads total - 1 maintainer
Top 0.6% on bioconductor.org
14 versions - Latest release: about 1 month ago - 181 dependent packages - 3.03 million downloads total - 4 maintainers
edgeR 4.2.0
Empirical Analysis of Digital Gene Expression Data in R14 versions - Latest release: about 1 month ago - 181 dependent packages - 3.03 million downloads total - 4 maintainers
Top 0.3% on bioconductor.org
5 versions - Latest release: about 1 month ago - 322 dependent packages - 5.11 million downloads total - 1 maintainer
limma 3.60.0
Linear Models for Microarray Data5 versions - Latest release: about 1 month ago - 322 dependent packages - 5.11 million downloads total - 1 maintainer
lemur 1.0.5
Latent Embedding Multivariate Regression6 versions - Latest release: 5 months ago - 1.29 thousand downloads total - 73 stars on GitHub - 1 maintainer
RLSeq 1.6.0
RLSeq: An analysis package for R-loop mapping data3 versions - Latest release: 8 months ago - 2.39 thousand downloads total - 2 stars on GitHub - 1 maintainer
tidySummarizedExperiment 1.14.0
Brings SummarizedExperiment to the Tidyverse3 versions - Latest release: 21 days ago - 5 dependent packages - 10.5 thousand downloads total - 19 stars on GitHub - 1 maintainer
SpatialFeatureExperiment 1.6.1
Integrating SpatialExperiment with Simple Features in sf4 versions - Latest release: 23 days ago - 1 dependent package - 4.24 thousand downloads total - 21 stars on GitHub - 1 maintainer
getDEE2 1.12.0
Programmatic access to the DEE2 RNA expression dataset3 versions - Latest release: 7 months ago - 4.01 thousand downloads total - 4 stars on GitHub - 1 maintainer
scider 1.2.0
Spatial cell-type inter-correlation by density in R2 versions - Latest release: about 1 month ago - 1 thousand downloads total - 0 stars on GitHub - 1 maintainer
dreamlet 1.2.0
Scalable differential expression analysis of single cell transcriptomics datasets with complex st...3 versions - Latest release: 29 days ago - 1.3 thousand downloads total - 9 stars on GitHub - 1 maintainer
InterCellar 2.8.0
InterCellar: an R-Shiny app for interactive analysis and exploration of cell-cell communication i...3 versions - Latest release: 6 months ago - 4.35 thousand downloads total - 8 stars on GitHub - 1 maintainer
DEsingle 1.22.0
DEsingle for detecting three types of differential expression in single-cell RNA-seq data3 versions - Latest release: 6 months ago - 1 dependent package - 24.1 thousand downloads total - 29 stars on GitHub - 1 maintainer
roastgsa 1.0.0
Rotation based gene set analysis2 versions - Latest release: 7 months ago - 881 downloads total - 0 stars on GitHub - 1 maintainer
adverSCarial 1.0.0
adverSCarial, generate and analyze the vulnerability of scRNA-seq classifiers to adversarial attacks2 versions - Latest release: 7 months ago - 935 downloads total - 1 maintainer
SeqGate 1.12.0
Filtering of Lowly Expressed Features3 versions - Latest release: 6 months ago - 4.94 thousand downloads total - 0 stars on GitHub - 1 maintainer
GWENA 1.12.0
Pipeline for augmented co-expression analysis3 versions - Latest release: 6 months ago - 7.57 thousand downloads total - 18 stars on GitHub - 1 maintainer
MOGAMUN 1.12.0
MOGAMUN: A Multi-Objective Genetic Algorithm to Find Active Modules in Multiplex Biological Networks3 versions - Latest release: 6 months ago - 3.79 thousand downloads total - 12 stars on GitHub - 1 maintainer
cardelino 1.4.0
Clone Identification from Single Cell Data3 versions - Latest release: 7 months ago - 2.53 thousand downloads total - 54 stars on GitHub - 1 maintainer
Top 2.1% on bioconductor.org
5 versions - Latest release: 4 months ago - 62 dependent packages - 399 thousand downloads total - 1 maintainer
scran 1.30.2
Methods for Single-Cell RNA-Seq Data Analysis5 versions - Latest release: 4 months ago - 62 dependent packages - 399 thousand downloads total - 1 maintainer
calm 1.16.0
Covariate Assisted Large-scale Multiple testing3 versions - Latest release: 6 months ago - 4.59 thousand downloads total - 0 stars on GitHub - 1 maintainer
pathwayPCA 1.18.0
Integrative Pathway Analysis with Modern PCA Methodology and Gene Selection3 versions - Latest release: 6 months ago - 1 dependent package - 7.56 thousand downloads total - 11 stars on GitHub - 1 maintainer
RegionalST 1.0.1
Investigating regions of interest and performing cross-regional analysis with spatial transcripto...3 versions - Latest release: 5 months ago - 1.07 thousand downloads total - 1 maintainer
tomoda 1.12.0
Tomo-seq data analysis3 versions - Latest release: 6 months ago - 3.34 thousand downloads total - 0 stars on GitHub - 1 maintainer
MOMA 1.14.0
Multi Omic Master Regulator Analysis3 versions - Latest release: 6 months ago - 4.74 thousand downloads total - 5 stars on GitHub - 1 maintainer
Top 2.1% on bioconductor.org
3 versions - Latest release: 7 months ago - 41 dependent packages - 548 thousand downloads total - 1 maintainer
scuttle 1.12.0
Single-Cell RNA-Seq Analysis Utilities3 versions - Latest release: 7 months ago - 41 dependent packages - 548 thousand downloads total - 1 maintainer
Top 5.5% on bioconductor.org
3 versions - Latest release: 7 months ago - 6 dependent packages - 42.6 thousand downloads total - 205 stars on GitHub - 1 maintainer
splatter 1.26.0
Simple Simulation of Single-cell RNA Sequencing Data3 versions - Latest release: 7 months ago - 6 dependent packages - 42.6 thousand downloads total - 205 stars on GitHub - 1 maintainer
ILoReg 1.12.1
ILoReg: a tool for high-resolution cell population identification from scRNA-Seq data4 versions - Latest release: 3 months ago - 3.61 thousand downloads total - 4 stars on GitHub - 1 maintainer
CAGEfightR 1.22.0
Analysis of Cap Analysis of Gene Expression (CAGE) data using Bioconductor3 versions - Latest release: 6 months ago - 1 dependent package - 18.7 thousand downloads total - 8 stars on GitHub - 1 maintainer
CellMixS 1.18.0
Evaluate Cellspecific Mixing3 versions - Latest release: 6 months ago - 7.43 thousand downloads total - 6 stars on GitHub - 1 maintainer
scCB2 1.12.0
CB2 improves power of cell detection in droplet-based single-cell RNA sequencing data3 versions - Latest release: 6 months ago - 3.98 thousand downloads total - 10 stars on GitHub - 1 maintainer
pram 1.18.0
Pooling RNA-seq datasets for assembling transcript models3 versions - Latest release: 7 months ago - 5.49 thousand downloads total - 1 stars on GitHub - 1 maintainer
BASiCS 2.14.0
Bayesian Analysis of Single-Cell Sequencing data3 versions - Latest release: 6 months ago - 2 dependent packages - 17.3 thousand downloads total - 83 stars on GitHub - 1 maintainer
OmicsLonDA 1.18.0 removed
Omics Longitudinal Differential Analysis2 versions - Latest release: 6 months ago - 5.95 thousand downloads total - 5 stars on GitHub - 1 maintainer
Top 2.1% on bioconductor.org
3 versions - Latest release: 6 months ago - 6 dependent packages - 161 thousand downloads total - 218 stars on GitHub - 1 maintainer
MAST 1.28.0
Model-based Analysis of Single Cell Transcriptomics3 versions - Latest release: 6 months ago - 6 dependent packages - 161 thousand downloads total - 218 stars on GitHub - 1 maintainer
orthogene 1.8.0
Interspecies gene mapping3 versions - Latest release: 7 months ago - 1 dependent package - 10.4 thousand downloads total - 35 stars on GitHub - 1 maintainer
switchde 1.28.0
Switch-like differential expression across single-cell trajectories3 versions - Latest release: 6 months ago - 10.6 thousand downloads total - 19 stars on GitHub - 1 maintainer
standR 1.6.0
Spatial transcriptome analyses of Nanostring's DSP data in R3 versions - Latest release: 6 months ago - 3.38 thousand downloads total - 15 stars on GitHub - 1 maintainer
Top 4.7% on bioconductor.org
4 versions - Latest release: 6 months ago - 80.3 thousand downloads total - 502 stars on GitHub - 1 maintainer
infercnv 1.18.1
Infer Copy Number Variation from Single-Cell RNA-Seq Data4 versions - Latest release: 6 months ago - 80.3 thousand downloads total - 502 stars on GitHub - 1 maintainer
Top 2.3% on bioconductor.org
3 versions - Latest release: 7 months ago - 13 dependent packages - 360 thousand downloads total - 130 stars on GitHub - 1 maintainer
tximport 1.30.0
Import and summarize transcript-level estimates for transcript- and gene-level analysis3 versions - Latest release: 7 months ago - 13 dependent packages - 360 thousand downloads total - 130 stars on GitHub - 1 maintainer
DESpace 1.2.1
DESpace: a framework to discover spatially variable genes4 versions - Latest release: 3 months ago - 1.47 thousand downloads total - 3 stars on GitHub - 1 maintainer
autonomics 1.12.0
Unified statistal Modeling of Omics Data4 versions - Latest release: 27 days ago - 3.18 thousand downloads total - 3 stars on GitHub - 1 maintainer
maser 1.20.0
Mapping Alternative Splicing Events to pRoteins3 versions - Latest release: 7 months ago - 10.9 thousand downloads total - 16 stars on GitHub - 1 maintainer
Top 4.4% on bioconductor.org
4 versions - Latest release: 18 days ago - 5 dependent packages - 197 thousand downloads total - 162 stars on GitHub - 1 maintainer
SingleR 2.6.0
Reference-Based Single-Cell RNA-Seq Annotation4 versions - Latest release: 18 days ago - 5 dependent packages - 197 thousand downloads total - 162 stars on GitHub - 1 maintainer
OmnipathR 3.10.1
OmniPath web service client and more3 versions - Latest release: 7 months ago - 3 dependent packages - 23.4 thousand downloads total - 1 maintainer
AlphaMissenseR 1.0.0
Accessing AlphaMissense Data Resources in R2 versions - Latest release: about 1 month ago - 358 downloads total - 5 stars on GitHub - 1 maintainer
epidecodeR 1.10.0
epidecodeR: a functional exploration tool for epigenetic and epitranscriptomic regulation3 versions - Latest release: 7 months ago - 2.79 thousand downloads total - 3 stars on GitHub - 1 maintainer
pengls 1.8.0
Fit Penalised Generalised Least Squares models3 versions - Latest release: 7 months ago - 2.06 thousand downloads total - 0 stars on GitHub - 1 maintainer
quantiseqr 1.10.0
Quantification of the Tumor Immune contexture from RNA-seq data3 versions - Latest release: 7 months ago - 2 dependent packages - 11.8 thousand downloads total - 1 maintainer
bacon 1.30.0
Controlling bias and inflation in association studies using the empirical null distribution3 versions - Latest release: 7 months ago - 16.9 thousand downloads total - 1 maintainer
deconvR 1.8.0
Simulation and Deconvolution of Omic Profiles3 versions - Latest release: 7 months ago - 3.22 thousand downloads total - 9 stars on GitHub - 1 maintainer
IsoformSwitchAnalyzeR 2.2.0
Identify, Annotate and Visualize Isoform Switches with Functional Consequences from both short- a...3 versions - Latest release: 7 months ago - 28.3 thousand downloads total - 1 maintainer
tLOH 1.10.0
Assessment of evidence for LOH in spatial transcriptomics pre-processed data using Bayes factor c...3 versions - Latest release: 7 months ago - 2.68 thousand downloads total - 3 stars on GitHub - 1 maintainer
satuRn 1.10.0
Scalable Analysis of Differential Transcript Usage for Bulk and Single-Cell RNA-sequencing Applic...3 versions - Latest release: 7 months ago - 1 dependent package - 7.57 thousand downloads total - 20 stars on GitHub - 1 maintainer
SPONGE 1.24.0
Sparse Partial Correlations On Gene Expression3 versions - Latest release: 7 months ago - 2 dependent packages - 8.57 thousand downloads total - 1 maintainer
MetaNeighbor 1.22.0
Single cell replicability analysis3 versions - Latest release: 7 months ago - 10 thousand downloads total - 1 maintainer
NanoStringNCTools 1.10.1
NanoString nCounter Tools4 versions - Latest release: about 1 month ago - 2 dependent packages - 14.3 thousand downloads total - 1 maintainer
megadepth 1.12.0
megadepth: BigWig and BAM related utilities3 versions - Latest release: 7 months ago - 2 dependent packages - 6.86 thousand downloads total - 11 stars on GitHub - 1 maintainer
tenXplore 1.24.0
ontological exploration of scRNA-seq of 1.3 million mouse neurons from 10x genomics3 versions - Latest release: 7 months ago - 8.35 thousand downloads total - 1 maintainer
phantasus 1.22.2
Visual and interactive gene expression analysis3 versions - Latest release: 7 months ago - 11 thousand downloads total - 1 maintainer
netboost 2.10.0
Network Analysis Supported by Boosting3 versions - Latest release: 7 months ago - 4.72 thousand downloads total - 1 maintainer
scMultiSim 1.0.0
Simulation of Multi-Modality Single Cell Data Guided By Gene Regulatory Networks and Cell-Cell In...1 version - Latest release: about 1 month ago - 144 downloads total - 18 stars on GitHub - 1 maintainer
lute 1.0.0
Framework for cell size scale factor normalized bulk transcriptomics deconvolution experiments1 version - Latest release: about 1 month ago - 340 downloads total - 2 stars on GitHub - 1 maintainer
omicsPrint 1.22.0
Cross omic genetic fingerprinting3 versions - Latest release: 7 months ago - 7.42 thousand downloads total - 1 maintainer
rScudo 1.18.1
Signature-based Clustering for Diagnostic Purposes4 versions - Latest release: 3 months ago - 5.75 thousand downloads total - 3 stars on GitHub - 1 maintainer
HumanTranscriptomeCompendium 1.17.0
Tools to work with a Compendium of 181000 human transcriptome sequencing studies3 versions - Latest release: 7 months ago - 5.69 thousand downloads total - 1 maintainer
txcutr 1.8.0
Transcriptome CUTteR3 versions - Latest release: 7 months ago - 2.26 thousand downloads total - 1 maintainer
stJoincount 1.4.0
stJoincount - Join count statistic for quantifying spatial correlation between clusters3 versions - Latest release: 7 months ago - 1.81 thousand downloads total - 5 stars on GitHub - 1 maintainer
geva 1.10.0
Gene Expression Variation Analysis (GEVA)3 versions - Latest release: 7 months ago - 2.79 thousand downloads total - 2 stars on GitHub - 1 maintainer
ISLET 1.4.0
Individual-Specific ceLl typE referencing Tool3 versions - Latest release: 7 months ago - 1.63 thousand downloads total - 1 maintainer
consensusOV 1.24.0
Gene expression-based subtype classification for high-grade serous ovarian cancer3 versions - Latest release: 7 months ago - 1 dependent package - 9.83 thousand downloads total - 1 maintainer
ccImpute 1.4.0
ccImpute: an accurate and scalable consensus clustering based approach to impute dropout events i...3 versions - Latest release: 7 months ago - 1.65 thousand downloads total - 1 stars on GitHub - 1 maintainer
MetaVolcanoR 1.16.0
Gene Expression Meta-analysis Visualization Tool3 versions - Latest release: 7 months ago - 10.5 thousand downloads total - 1 maintainer
ppcseq 1.10.0
Probabilistic Outlier Identification for RNA Sequencing Generalized Linear Models3 versions - Latest release: 7 months ago - 2.85 thousand downloads total - 6 stars on GitHub - 1 maintainer
Voyager 1.4.0
From geospatial to spatial omics3 versions - Latest release: 7 months ago - 2.86 thousand downloads total - 60 stars on GitHub - 1 maintainer
CONSTANd 1.10.0
Data normalization by matrix raking3 versions - Latest release: 7 months ago - 3.41 thousand downloads total - 1 maintainer
FLAMES 1.8.0
FLAMES: Full Length Analysis of Mutations and Splicing in long read RNA-seq data3 versions - Latest release: 7 months ago - 4.98 thousand downloads total - 7 stars on GitHub - 1 maintainer
phenomis 1.4.0
Postprocessing and univariate analysis of omics data3 versions - Latest release: 7 months ago - 1.98 thousand downloads total - 1 maintainer
CTdata 1.2.0
Data companion to CTexploreR3 versions - Latest release: 7 months ago - 1 dependent package - 1.24 thousand downloads total - 1 stars on GitHub - 1 maintainer
diffuStats 1.22.0
Diffusion scores on biological networks3 versions - Latest release: 7 months ago - 9.33 thousand downloads total - 1 maintainer
omicplotR 1.22.0
Visual Exploration of Omic Datasets Using a Shiny App3 versions - Latest release: 7 months ago - 8.13 thousand downloads total - 1 maintainer
Spaniel 1.16.0
Spatial Transcriptomics Analysis3 versions - Latest release: 7 months ago - 6.46 thousand downloads total - 1 maintainer
Related Keywords
Software
243
GeneExpression
167
RNASeq
141
SingleCell
100
Sequencing
97
DifferentialExpression
75
ImmunoOncology
67
Transcription
61
Clustering
56
Visualization
49
Normalization
42
Regression
38
DimensionReduction
35
DataImport
34
Preprocessing
34
Spatial
30
SystemsBiology
29
GeneSetEnrichment
27
QualityControl
27
Classification
27
Coverage
23
Proteomics
23
MultipleComparison
22
BiomedicalInformatics
21
FunctionalGenomics
21
Microarray
21
GeneRegulation
21
Genetics
20
Network
20
FeatureExtraction
19
Epigenetics
18
DataRepresentation
18
r
18
Bayesian
18
transcriptomics
17
AlternativeSplicing
16
BatchEffect
16
GraphAndNetwork
16
bioconductor
15
Pathways
14
DifferentialSplicing
13
StatisticalMethod
13
PrincipalComponent
13
Metabolomics
13
Annotation
12
mRNAMicroarray
12
Infrastructure
12
CellBiology
11
rna-seq
11
GUI
11
single-cell
10
CellBasedAssays
10
TimeCourse
9
bioinformatics
8
r-package
8
genomics
8
DNAMethylation
8
NetworkInference
8
bioconductor-package
8
rstats
8
GO
7
KEGG
7
gene-expression
7
FunctionalPrediction
6
ProprietaryPlatforms
6
human-cell-atlas
6
scrna-seq
6
Survival
6
ChIPSeq
6
Alignment
6
WorkflowStep
6
GeneTarget
6
MassSpectrometry
5
GenomeAnnotation
5
single-cell-rna-seq
5
NetworkEnrichment
5
ExperimentalDesign
5
SupportVectorMachine
5
AssayDomain
5
GenePrediction
5
GenomicVariation
5
bayesian
4
Reactome
4
ExonArray
4
SNP
4
tidyverse
4
MicroRNAArray
4
Lipidomics
4
ExperimentHubSoftware
4
ReportWriting
4
GenomeWideAssociation
4
GeneSignaling
4
CopyNumberVariation
4
DNASeq
4
ShinyApps
4
DifferentialMethylation
4
clustering
4
Cheminformatics
3
ResearchField
3
FlowCytometry
3