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God made everything out of nothing. But the nothingness shows through.
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GraphBio: A shiny web app to easily perform popular visualization analysis for omics data
21
577
3K
ggcoverage: an R package to visualize and annotate genome coverage for various NGS data
14
567
3K
GraphBio: A shiny web app to easily perform popular visualization analysis for omics data
8
273
1K
plotsr: Visualising structural similarities and rearrangements between multiple genomes
8
196
887
GenoFig: a user-friendly application for the visualisation and comparison of genomic regions
4
198
814
Gos: a declarative library for interactive genomics visualization in Python
4
174
684
ggcoverage: an R package to visualize and annotate genome coverage for various NGS data
4
105
618
SpaceX: Gene Co-expression Network Estimation for Spatial Transcriptomics
1
147
602
Gos: a declarative library for interactive genomics visualization in Python
3
137
559
gget: Efficient querying of genomic databases for single-cell RNA-seq
4
152
563
RNAlysis: analyze your RNA sequencing data without writing a single line of code
3
130
556
Read2Tree: scalable and accurate phylogenetic trees from raw reads
2
130
528
JBrowse 2: A modular genome browser with views of synteny and structural variation
3
99
528
PyDESeq2: a python package for bulk RNA-seq differential expression analysis
2
113
495
PlotS: web-based application for data visualization and analysis
4
121
461
Ggkegg: analysis and visualization of KEGG data utilizing grammar of graphics
0
116
453
Many bioinformatics programming tasks can be automated with ChatGPT
5
111
435
hdWGCNA: High dimensional co-expression networks enable discovery of transcriptomic drivers in complex biological systems
4
93
421
DeepBIO: an automated and interpretable deep-learning platform for high-throughput biological sequence prediction, functional annotation and visualization analysis
2
104
423
Igv.js: an embeddable JavaScript implementation of the Integrative Genomics Viewer (IGV)
2
59
407
ChromoMap: an R package for interactive visualization of multi-omics data and annotation of chromosomes
1
98
376
BioNumPy: Fast and easy analysis of biological data with Python
1
63
369
multiWGCNA: an R package for deep mining gene co-expression networks in multi-trait expression data
1
96
372
phytools 2.0: An updated R ecosystem for phylogenetic comparative methods (and other things)
0
103
357
DeepBIO is an automated and interpretable deep-learning platform for biological sequence prediction, functional annotation, and visualization analysis
1
80
352
Tree2GD: A Phylogenomic Method to Detect Large Scale Gene Duplication Events
3
92
355
ggcoverage: an R package to visualize and annotate genome coverage for various NGS data
2
66
315
PyGenePlexus: A Python package for gene discovery using network-based machine learning
4
74
302
BioNumPy: Fast and easy analysis of biological data with Python
1
54
292
BiomiX: a User-Friendly Bioinformatic Tool for Automatized Multiomics Data Analysis and Integration
2
85
292
Cellsnake: a user-friendly tool for single-cell RNA sequencing analysis
0
76
292
LotOfCells: data visualization and statistics of single cell metadata
2
67
290
nanoSHAPE: Direct detection of RNA modifications and structure using single molecule nanopore sequencing
2
104
289
Transcription factor expression is the main determinant of variability in gene co-activity
0
54
280
xcore: an R package for inference of gene expression regulators
2
66
282
PyWGCNA: A Python package for weighted gene co-expression network analysis
2
79
276
scGSEA / scMAP: Single-cell gene set enrichment analysis and transfer learning for functional annotation of scRNA-seq data
2
74
272
Igv.js: an embeddable JavaScript implementation of the Integrative Genomics Viewer (IGV)
2
60
274
GPTCelltype: Assessing GPT-4 for cell type annotation in single-cell RNA-seq analysis
3
68
265
DeepCOLOR: Single-cell colocalization analysis using a deep generative model
2
57
264
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
258
NGenomeSyn: an easy-to-use and flexible tool for publication-ready visualization of syntenic relationships across multiple genomes
3
58
255
CuteSV: Structural Variant Detection from Long-Read Sequencing Data
2
61
254
GW: ultra-fast chromosome-scale visualisation of genomics data
3
66
254
NGenomeSyn: an easy-to-use and flexible tool for publication-ready visualization of syntenic relationships across multiple genomes
0
75
253
PCA-Plus: Enhanced principal component analysis with illustrative applications to batch effects and their quantitation
1
68
242
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
63
246
scMTNI: Inference of cell type-specific gene regulatory networks on cell lineages from single cell omic datasets
1
49
239
SpaTalk: Knowledge-graph-based cell-cell communication inference for spatially resolved transcriptomic data
2
53
243
SYNY: a pipeline to investigate and visualize collinearity between genomes
3
72
237
syntenet: an R/Bioconductor package for the inference and analysis of synteny networks
0
54
235
Syntenet: an R/Bioconductor package for the inference and analysis of synteny networks
2
56
231
GENELink: Graph attention network for link prediction of gene regulations from single cell RNA-sequencing data
1
45
230
Bioinformatics Copilot 1.0: A Large Language Model-powered Software for the Analysis of Transcriptomic Data
3
65
230
Census: accurate, automated, deep, fast, and hierarchical scRNA-seq cell-type annotation
3
48
226
Single Cell Atlas: a single-cell multi-omics human cell encyclopedia
0
70
224
Transformers in single-cell omics: a review and new perspectives
2
63
221
LongPhase: an ultra-fast chromosome-scale phasing algorithm for small and large variants
0
64
225
Boosting single-cell gene regulatory network reconstruction via bulk-cell transcriptomic data
2
33
219
scMEGA: Single-cell Multiomic Enhancer-based Gene Regulatory Network Inference
0
35
215
Syntenet: an R/Bioconductor package for the inference and analysis of synteny networks
0
54
219
VCF2PCACluster: a simple, fast and memory-efficient tool for principal component analysis of tens of millions of SNPs
0
57
217
rGREAT: an R/Bioconductor package for functional enrichment on genomic regions
0
47
217
In silico methods for predicting functional synonymous variants
4
65
215
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.
3
19
210
scverse: Foundational tools for omics data in the life sciences
1
31
214
Figeno: multi-region genomic figures with long-read support
2
58
212
networkGWAS: A network-based approach to discover genetic associations
1
55
208
MuSiC2: cell type deconvolution for multi-condition bulk RNA-seq data
2
48
207
HiMAP2: Identifying phylogenetically informative genetic markers from diverse genomic resources
0
53
206
memento: Generalized differential expression analysis of single-cell RNA-seq with method of moments estimation and efficient resampling
1
37
202
PyWGCNA: A Python package for weighted gene co-expression network analysis
1
58
202
networkGWAS: A network-based approach to discover genetic associations
3
59
201
Visual Omics: A web-based platform for omics data analysis and visualization with rich graph-tuning capabilities
0
58
201
Treenome Browser: co-visualization of enormous phylogenies and millions of genomes
3
57
195
compare_genomes: a comparative genomics workflow to streamline the analysis of evolutionary divergence across genomes
1
45
198
Reference-free and cost-effective automated cell type annotation with GPT-4 in single-cell RNA-seq analysis
2
48
196
ENCODE-rE2G: An encyclopedia of enhancer-gene regulatory interactions in the human genome
0
48
187
SpaceX: Gene Co-expression Network Estimation for Spatial Transcriptomics
2
20
192
simona: a Comprehensive R package for Semantic Similarity Analysis on Bio-Ontologies
2
51
189
macrosyntR : Drawing automatically ordered Oxford Grids from standard genomic files in R
0
44
193
LiftOn: Combining DNA and protein alignments to improve genome annotation
1
65
189
Haplotype-resolved assembly of diploid genomes without parental data
0
53
191