22 results found Sort:

seandavi
awesome-single-cell seandavi
929
3.0k
mit
249
Community-curated list of software packages and data resources for single-cell, including RNA-seq, ATAC-seq, etc.
python analysis atac-seq cell-cycle clustering single-cell awesome-list rna-seq-data cell-clusters bioinformatics scrna-seq-data gene-expression cell-populations data-integration analysis-pipeline data-visualization rna-seq-experiments cell-differentiation dimensionality-reduction gene-expression-profiles
Created 2016-06-29
743 commits to master branch, last one 2 months ago
COMBINE-lab
salmon COMBINE-lab
160
739
gpl-3.0
39
🐟 🍣 🍱 Highly-accurate & wicked fast transcript-level quantification from RNA-seq reads using selective alignment
10x rnaseq salmon rna-seq sailfish scrna-seq c-plus-plus single-cell quasi-mapping transcriptome bioinformatics quantification gene-expression selective-alignment single-cell-rna-seq rna-seq-quantification
Created 2015-03-19
1,907 commits to master branch, last one 2 months ago
saeyslab
nichenetr saeyslab
113
441
unknown
15
NicheNet: predict active ligand-target links between interacting cells
rna-seq ligand-target gene-expression ligand-receptor data-integration network-inference single-cell-omics single-cell-rna-seq cell-cell-communication intercellular-communication
Created 2018-02-05
465 commits to master branch, last one a day ago
lucidrains
enformer-pytorch lucidrains
69
399
mit
17
Implementation of Enformer, Deepmind's attention network for predicting gene expression, in Pytorch
genomics transformer deep-learning dna-sequences gene-expression attention-mechanism artificial-intelligence
Created 2021-10-23
172 commits to main branch, last one 5 months ago
broadinstitute
Tangram broadinstitute
45
224
bsd-3-clause
12
Spatial alignment of single cell transcriptomic data.
visium scrna-seq snrna-seq spatial-data gene-expression computational-biology
Created 2020-08-21
299 commits to master branch, last one about a year ago
iSEE
iSEE iSEE
41
220
mit
17
R/shiny interface for interactive visualization of data in SummarizedExperiment objects
gui shiny clustering single-cell hacktoberfest visualization gene-expression transcriptomics human-cell-atlas feature-extraction dimension-reduction
Created 2017-12-06
3,224 commits to devel branch, last one about a month ago
junjunlab
ClusterGVis junjunlab
16
185
mit
4
One-step to Cluster and Visualize Gene Expression Matrix
mfuzz visualization complexheatmap gene-clustering gene-expression
Created 2022-11-19
111 commits to main branch, last one 4 days ago
fbrundu
pymrmr fbrundu
37
138
mit
2
Python3 binding to mRMR Feature Selection algorithm (currently not maintained)
data-science gene-expression feature-selection mutual-information computational-biology
Created 2017-03-09
228 commits to master branch, last one 3 years ago
federicomarini
awesome-expression-browser federicomarini
37
124
mit
17
😎 A curated list of software and resources for exploring and visualizing (browsing) expression data 😎
atlas awesome-list rna-seq-data bioinformatics humancellatlas gene-expression data-exploration data-visualization expression-browser gene-expression-profiles
Created 2019-03-30
186 commits to master branch, last one about a month ago
saezlab
dorothea saezlab
25
121
gpl-3.0
15
R package to access DoRothEA's regulons
regulons tf-activities gene-expression functional-analysis bioconductor-package transcription-factor
Created 2017-03-27
282 commits to master branch, last one 3 months ago
bvieth
powsimR bvieth
23
103
artistic-2.0
8
Power analysis is essential to optimize the design of RNA-seq experiments and to assess and compare the power to detect differentially expressed genes. PowsimR is a flexible tool to simulate and evalu...
r power rna-seq simulation single-cell power-analysis gene-expression experimental-design simulation-framework
Created 2017-04-16
82 commits to master branch, last one 10 months ago
catavallejos
BASiCS catavallejos
16
82
unknown
7
BASiCS: Bayesian Analysis of Single-Cell Sequencing Data. This is an unstable experimental version. Please see http://bioconductor.org/packages/BASiCS/ for the official release version
r rcpp bayesian scrna-seq single-cell rcpparmadillo gene-expression bioconductor-package
Created 2015-05-19
1,003 commits to devel branch, last one 2 months ago
lucidrains
tf-bind-transformer lucidrains
9
78
mit
8
A repository with exploration into using transformers to predict DNA ↔ transcription factor binding
transformers deep-learning gene-expression attention-mechanism transcription-factors artificial-intelligence transcription-factor-binding
Created 2021-12-08
234 commits to main branch, last one about a year ago
federicomarini
GeneTonic federicomarini
8
75
other
6
Enjoy your transcriptomic data and analysis responsibly - like sipping a cocktail
r gui shiny bioconductor rna-seq-data transcriptome user-friendly gene-expression transcriptomics data-exploration pathway-analysis rna-seq-analysis data-visualization bioconductor-package reproducible-research functional-enrichment-analysis
Created 2019-06-24
1,069 commits to devel branch, last one 29 days ago
GfellerLab
EPIC GfellerLab
21
70
other
5
Repository for the R package EPIC, to Estimate the Proportion of Immune and Cancer cells from bulk gene expression data.
rna-seq bulk-data cell-type cancer-cells gene-expression
Created 2017-01-18
28 commits to master branch, last one 10 months ago
aertslab
SCope aertslab
14
68
gpl-3.0
9
Fast visualization tool for large-scale and high dimensional single-cell data
aws grpc loom cloud reactjs single-cell gene-expression gene-regulatory-network large-scale-data-visualization
Created 2018-02-13
1,617 commits to master branch, last one 2 years ago
greenelab
BioBombe greenelab
23
63
bsd-3-clause
6
BioBombe: Sequentially compressed gene expression features enhances biological signatures
tcga hetnet msigdb network biobombe gene-sets autoencoder compression gene-expression
Created 2018-03-22
234 commits to master branch, last one 3 years ago
AAlhendi1707
countToFPKM AAlhendi1707
14
60
gpl-3.0
3
Convert Counts to Fragments per Kilobase of Transcript per Million (FPKM)
rna-seq normalization gene-expression
Created 2019-03-23
172 commits to master branch, last one 3 years ago
COMBINE-lab
terminus COMBINE-lab
3
55
bsd-3-clause
6
This repository has no description...
rna-seq gene-expression transcriptomics
Created 2020-01-30
56 commits to master branch, last one 2 years ago
JEFworks-Lab
MERINGUE JEFworks-Lab
5
52
gpl-3.0
4
characterizing spatial gene expression heterogeneity in spatially resolved single-cell transcriptomics data with nonuniform cellular densities
rstats single-cell gene-expression spatial-analysis cell-cell-communication spatial-transcriptomics
Created 2018-04-26
184 commits to master branch, last one about a year ago
ezgisubasi
breast-cancer-gene-expression ezgisubasi
4
38
unknown
4
This project aims to predict people who will survive breast cancer using machine learning models with the help of clinical data and gene expression profiles of the patients.
breast-cancer data-analysis gene-expression machine-learning data-visualization breast-cancer-classification
Created 2021-05-30
42 commits to main branch, last one 2 years ago
gaolabtools
scNanoGPS gaolabtools
1
33
other
4
Single cell Nanopore sequencing data for Genotype and Phenotype
isoforms single-cell cell-barcode umi-curation demultiplexing gene-expression rna-seq-pipeline long-read-sequencing nanopore-analysis-pipeline single-nucleotide-variation
Created 2022-09-13
30 commits to v1.1 branch, last one 3 days ago