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GraphBio: A shiny web app to easily perform popular visualization analysis for omics data
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550
3K
ggcoverage: an R package to visualize and annotate genome coverage for various NGS data
14
530
3K
GraphBio: A shiny web app to easily perform popular visualization analysis for omics data
8
275
1K
plotsr: Visualising structural similarities and rearrangements between multiple genomes
8
179
841
Gos: a declarative library for interactive genomics visualization in Python
3
154
641
ggcoverage: an R package to visualize and annotate genome coverage for various NGS data
4
105
622
SpaceX: Gene Co-expression Network Estimation for Spatial Transcriptomics
1
142
597
Gos: a declarative library for interactive genomics visualization in Python
3
137
563
gget: Efficient querying of genomic databases for single-cell RNA-seq
4
153
566
RNAlysis: analyze your RNA sequencing data without writing a single line of code
3
132
555
JBrowse 2: A modular genome browser with views of synteny and structural variation
3
99
532
Read2Tree: scalable and accurate phylogenetic trees from raw reads
2
119
500
PyDESeq2: a python package for bulk RNA-seq differential expression analysis
2
104
469
PlotS: web-based application for data visualization and analysis
4
114
447
Many bioinformatics programming tasks can be automated with ChatGPT
4
110
427
hdWGCNA: High dimensional co-expression networks enable discovery of transcriptomic drivers in complex biological systems
4
94
425
Ggkegg: analysis and visualization of KEGG data utilizing grammar of graphics
0
101
422
DeepBIO: an automated and interpretable deep-learning platform for high-throughput biological sequence prediction, functional annotation and visualization analysis
2
103
416
Igv.js: an embeddable JavaScript implementation of the Integrative Genomics Viewer (IGV)
2
54
400
ChromoMap: an R package for interactive visualization of multi-omics data and annotation of chromosomes
1
98
378
DeepBIO is an automated and interpretable deep-learning platform for biological sequence prediction, functional annotation, and visualization analysis
1
80
354
Tree2GD: A Phylogenomic Method to Detect Large Scale Gene Duplication Events
3
92
354
phytools 2.0: An updated R ecosystem for phylogenetic comparative methods (and other things)
0
98
350
multiWGCNA: an R package for deep mining gene co-expression networks in multi-trait expression data
1
83
345
BioNumPy: Fast and easy analysis of biological data with Python
1
54
339
ggcoverage: an R package to visualize and annotate genome coverage for various NGS data
2
65
316
PyGenePlexus: A Python package for gene discovery using network-based machine learning
4
76
302
BioNumPy: Fast and easy analysis of biological data with Python
1
54
296
nanoSHAPE: Direct detection of RNA modifications and structure using single molecule nanopore sequencing
2
104
292
Transcription factor expression is the main determinant of variability in gene co-activity
0
55
284
Cellsnake: a user-friendly tool for single-cell RNA sequencing analysis
0
69
280
PyWGCNA: A Python package for weighted gene co-expression network analysis
2
80
278
scGSEA / scMAP: Single-cell gene set enrichment analysis and transfer learning for functional annotation of scRNA-seq data
2
75
274
Igv.js: an embeddable JavaScript implementation of the Integrative Genomics Viewer (IGV)
2
61
274
GPTCelltype: Assessing GPT-4 for cell type annotation in single-cell RNA-seq analysis
3
69
268
xcore: an R package for inference of gene expression regulators
2
64
267
DeepCOLOR: Single-cell colocalization analysis using a deep generative model
2
58
266
PanGenie: Pangenome-based genome inference allows efficient and accurate genotyping across a wide spectrum of variant classes
3
61
259
PyGenePlexus: A Python package for gene discovery using network-based machine learning
3
58
260
CuteSV: Structural Variant Detection from Long-Read Sequencing Data
2
61
255
PCA-Plus: Enhanced principal component analysis with illustrative applications to batch effects and their quantitation
1
70
247
Minigraph-Cactus: Pangenome Graph Construction from Genome Alignment
1
66
249
Transposable element finder (TEF): finding active transposable elements from next generation sequencing data
2
64
246
NGenomeSyn: an easy-to-use and flexible tool for publication-ready visualization of syntenic relationships across multiple genomes
3
48
243
scMTNI: Inference of cell type-specific gene regulatory networks on cell lineages from single cell omic datasets
1
51
239
SpaTalk: Knowledge-graph-based cell-cell communication inference for spatially resolved transcriptomic data
2
55
243
SYNY: a pipeline to investigate and visualize collinearity between genomes
3
71
239
syntenet: an R/Bioconductor package for the inference and analysis of synteny networks
0
54
237
NGenomeSyn: an easy-to-use and flexible tool for publication-ready visualization of syntenic relationships across multiple genomes
0
67
235
GENELink: Graph attention network for link prediction of gene regulations from single cell RNA-sequencing data
1
45
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Census: accurate, automated, deep, fast, and hierarchical scRNA-seq cell-type annotation
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52
227
Bioinformatics Copilot 1.0: A Large Language Model-powered Software for the Analysis of Transcriptomic Data
3
65
228
Single Cell Atlas: a single-cell multi-omics human cell encyclopedia
0
70
226
LongPhase: an ultra-fast chromosome-scale phasing algorithm for small and large variants
0
64
224
Syntenet: an R/Bioconductor package for the inference and analysis of synteny networks
2
46
220
Boosting single-cell gene regulatory network reconstruction via bulk-cell transcriptomic data
2
34
220
scMEGA: Single-cell Multiomic Enhancer-based Gene Regulatory Network Inference
0
36
216
VCF2PCACluster: a simple, fast and memory-efficient tool for principal component analysis of tens of millions of SNPs
0
58
218
Syntenet: an R/Bioconductor package for the inference and analysis of synteny networks
0
54
219
rGREAT: an R/Bioconductor package for functional enrichment on genomic regions
0
48
217
In silico methods for predicting functional synonymous variants
4
64
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scverse: Foundational tools for omics data in the life sciences
1
31
213
BioNumPy is able to efficiently load biological datasets (e.g. FASTQ-files, BED-files and BAM-files) into NumPy-like data structures, so that NumPy operations like indexing, vectorized functions and reductions can be applied to the data.
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19
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networkGWAS: A network-based approach to discover genetic associations
1
56
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MuSiC2: cell type deconvolution for multi-condition bulk RNA-seq data
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48
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HiMAP2: Identifying phylogenetically informative genetic markers from diverse genomic resources
0
52
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memento: Generalized differential expression analysis of single-cell RNA-seq with method of moments estimation and efficient resampling
1
38
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networkGWAS: A network-based approach to discover genetic associations
3
56
201
compare_genomes: a comparative genomics workflow to streamline the analysis of evolutionary divergence across genomes
1
44
199
Visual Omics: A web-based platform for omics data analysis and visualization with rich graph-tuning capabilities
0
57
196
Reference-free and cost-effective automated cell type annotation with GPT-4 in single-cell RNA-seq analysis
2
48
195
SpaceX: Gene Co-expression Network Estimation for Spatial Transcriptomics
2
21
194
Haplotype-resolved assembly of diploid genomes without parental data
0
53
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LiftOn: Combining DNA and protein alignments to improve genome annotation
1
65
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macrosyntR : Drawing automatically ordered Oxford Grids from standard genomic files in R
0
44
191
compare_genomes: a comparative genomics workflow to streamline the analysis of evolutionary divergence across genomes
0
44
189
NetAct: a computational platform to construct core transcription factor regulatory networks using gene activity
0
49
189
SNPLift: Fast and accurate conversion of genetic variant coordinates across genome assemblies
2
40
187
CAMLU: A machine learning-based method for automatically identifying novel cells in annotating single cell RNA-seq data
1
56
184
Treenome Browser: co-visualization of enormous phylogenies and millions of genomes
3
52
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Comparative Genome Viewer: whole-genome eukaryotic alignments
1
52
187
exFINDER: identify external communication signals using single-cell transcriptomics data
1
44
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Dictys: dynamic gene regulatory network dissects developmental continuum with single-cell multi-omics
1
47
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NetAct: a computational platform to construct core transcription factor regulatory networks using gene activity
1
47
179
HiCoEx: Prediction of Gene Co-expression from Chromatin Contacts with Graph Attention Network
0
26
182
TBtools-II: A “one for all, all for one” bioinformatics platform for biological big-data mining
1
54
178