IgGeneUsage - Differential gene usage in immune repertoires

Detection of biases in the usage of immunoglobulin (Ig) genes is an important task in immune repertoire profiling. IgGeneUsage detects aberrant Ig gene usage between biological conditions using a probabilistic model which is analyzed computationally by Bayes inference. With this IgGeneUsage also avoids some common problems related to the current practice of null-hypothesis significance testing.

Last updated 24 days ago

differentialexpressionregressiongeneticsbayesianbiomedicalinformaticsimmunooncologymathematicalbiologyb-cell-receptorbcr-repertoiredifferential-analysisdifferential-gene-expressionhigh-throughput-sequencingimmune-repertoireimmune-repertoire-analysisimmune-repertoiresimmunogenomicsimmunoglobulinimmunoinformaticsimmunological-bioinformaticsimmunologytcr-repertoirevdj-recombination

6.19 score 6 stars 1 scripts 143 downloads

ClustIRR - Clustering of immune receptor repertoires

ClustIRR analyzes repertoires of B- and T-cell receptors. It starts by identifying communities of immune receptors with similar specificities, based on the sequences of their complementarity-determining regions (CDRs). Next, it employs a Bayesian probabilistic models to quantify differential community occupancy (DCO) between repertoires, allowing the identification of expanding or contracting communities in response to e.g. infection or cancer treatment.

Last updated 3 days ago

clusteringimmunooncologysinglecellsoftwareclassificationb-cell-receptorbioinformaticsimmunoinformaticsimmunologyquantitative-methodsrep-seqrepertoire-analysist-cell-receptor

5.92 score 2 stars 2 scripts 142 downloads

scBubbletree - Quantitative visual exploration of scRNA-seq data

scBubbletree is a quantitative method for the visual exploration of scRNA-seq data, preserving key biological properties such as local and global cell distances and cell density distributions across samples. It effectively resolves overplotting and enables the visualization of diverse cell attributes from multiomic single-cell experiments. Additionally, scBubbletree is user-friendly and integrates seamlessly with popular scRNA-seq analysis tools, facilitating comprehensive and intuitive data interpretation.

Last updated 24 days ago

visualizationclusteringsinglecelltranscriptomicsrnaseqbig-databigdatascrna-seqscrna-seq-analysisvisualvisual-exploration

5.82 score 6 stars 4 scripts 154 downloads