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transcriptomics
Here are 306 public repositories matching this topic...
An interactive explorer for single-cell transcriptomics data
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May 9, 2022 - JavaScript
MxMstrmn
commented
Aug 9, 2021
I was not aware how .h5ad stores their dicts and it took me quite a bit to figure out why my stored adata.uns['key'] was different from the original adata.uns['key']. Part of the problem was the large dataset which made examination of potential fail cases difficult.
Eventuelly, I figured out that some molecular descriptors include the sequence '(+/-)' which caused anndata to store the d
pySCENIC is a lightning-fast python implementation of the SCENIC pipeline (Single-Cell rEgulatory Network Inference and Clustering) which enables biologists to infer transcription factors, gene regulatory networks and cell types from single-cell RNA-seq data.
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Apr 22, 2022 - Python
R/shiny interface for interactive visualization of data in SummarizedExperiment objects
visualization
gui
shiny
clustering
gene-expression
feature-extraction
transcriptomics
single-cell
hacktoberfest
dimension-reduction
human-cell-atlas
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Apr 29, 2022 - R
The COnstraint-Based Reconstruction and Analysis Toolbox. Documentation:
tutorial
metabolomics
reconstruction
transcriptomics
cobra
metabolic-models
strain-engineering
metabolic-reconstruction
constraint-based-modeling
microbiome-analysis
metabolic-engineering
gap-filling
cobra-toolbox
omics-data-integration
human-metabolism
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May 3, 2022 - MATLAB
starfish: unified pipelines for image-based transcriptomics
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Apr 6, 2022 - Python
Single cell perturbation prediction
bioinformatics
deep-learning
generative-model
scrna-seq
transcriptomics
single-cell
single-cell-genomics
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Apr 25, 2022 - Python
R package for analyzing single-cell RNA-seq data
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Apr 5, 2020 - R
R package for analyzing and interactively exploring large-scale single-cell RNA-seq datasets
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Apr 19, 2022 - JavaScript
Fusing Histology and Genomics via Deep Learning - IEEE TMI
genomics
fusion
transcriptomics
pathology
multimodal
histopathology
computational-pathogenomics
pathomic
multimodal-network
mahmoodlab
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Mar 4, 2022 - Jupyter Notebook
Automatic Annotation on Cell Types of Clusters from Single-Cell RNA Sequencing Data
rna-seq
sequencing
transcriptome
transcriptomics
single-cell
marker-genes
seurat
cluster-annotation
cell-markers
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Apr 27, 2022 - R
Differential expression analysis for single-cell RNA-seq data.
bioinformatics
tensorflow
transcriptomics
gene-set-enrichment
differential-expression
single-cell-rna-seq
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May 3, 2022 - Python
Brings transcriptomics to the tidyverse
pipe
tidy-data
tidyverse
pca
bioconductor
deseq2
entrez
tidy
transcripts
transcriptomics
tsne
differential-expression
edger
redundancy
gsea
tibble
gene-symbols
bulk-transcriptional-analyses
mds-dimensions
ensembl-ids
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Apr 12, 2022 - R
Identification of differential RNA modifications from nanopore direct RNA sequencing
machine-learning
rna-seq
genomics
rna
transcriptomics
modification
nanopore-sequencing
rna-modifications
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Feb 10, 2022 - Python
A list of web-based interactive biological data visualizations.
visualization
awesome
medicine
genomics
cancer
biology
data-visualization
awesome-list
transcriptomics
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Apr 1, 2021
An ontology of cell types
genomics
semantic-web
owl
ontology
transcriptomics
anatomy
metazoa
obofoundry
cell-ontology
cell-types
anatomy-ontology
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May 10, 2022 - Makefile
HMM-integrated Bayesian approach for detecting CNV and LOH events from single-cell RNA-seq data
hmm
bioinformatics
bayesian
transcriptomics
subpopulation
heterogeneity
single-cell-rna-seq
single-cell-analysis
cnv-detection
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Jul 19, 2021 - R
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May 11, 2022 - Rust
A tool to identify, orient, trim and rescue full length cDNA reads
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Apr 27, 2022 - Python
Hierarchical, iterative clustering for analysis of transcriptomics data in R
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May 5, 2022 - R
Reference-guided transcript discovery and quantification for long read RNA-Seq data
r
bioconductor
transcriptomics
rna-seq-analysis
transcript-quantification
bambu
long-reads
nanopore-sequencing
transcript-reconstruction
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May 4, 2022 - R
Enjoy your transcriptomic data and analysis responsibly - like sipping a cocktail
gui
r
shiny
reproducible-research
gene-expression
data-visualization
bioconductor
transcriptome
user-friendly
data-exploration
transcriptomics
rna-seq-analysis
pathway-analysis
rna-seq-data
bioconductor-package
functional-enrichment-analysis
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May 1, 2022 - R
Cell-type Annotation for Single-cell Transcriptomics using Deep Learning with a Weighted Graph Neural Network
deep-learning
annotation
scrna-seq
transcriptomics
single-cell
cell-type-classification
gnn
graph-neural-network
reference-free
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Sep 10, 2021 - Python
Multi-sample Unified Discriminant ANalysis
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Apr 11, 2022 - R
Finding surprising needles (=genes) in haystacks (=single cell transcriptome data).
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May 10, 2022 - R
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May 5, 2022 - Rust
Tools to annotate genomes using long read transcriptomics data
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Dec 8, 2020 - Go
Nanopore RNA-Seq data from the Singapore Nanopore-Expression Project
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Nov 19, 2021
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In pl.pca_loagings(), there should be an option to limit the number of points plotted (basically n_points from ranking)
Why: I recently used the AnnData/scanpy suite to perform some analysis on a low number of genes (less than 30, amplified by qRT-PCR).
As the number of features is less than 30 (30 being the default value for n_points in ranking(adata,*args,**kwargs), the loadings appear twice