Peptides - Calculate Indices and Theoretical Physicochemical Properties of Protein Sequences

Includes functions to calculate several physicochemical properties and indices for amino-acid sequences as well as to read and plot 'XVG' output files from the 'GROMACS' molecular dynamics package.

Last updated 1 years ago

bioinformaticscalculate-indicespeptidesprotein-sequencesqsarcpp

9.06 score 82 stars 7 dependents 245 scripts 947 downloads

scTenifoldKnk - In-Silico Knockout Experiments from Single-Cell Gene Regulatory Networks

A workflow based on 'scTenifoldNet' to perform in-silico knockout experiments using single-cell RNA sequencing (scRNA-seq) data from wild-type (WT) control samples as input. First, the package constructs a single-cell gene regulatory network (scGRN) and knocks out a target gene from the adjacency matrix of the WT scGRN by setting the gene’s outdegree edges to zero. Then, it compares the knocked out scGRN with the WT scGRN to identify differentially regulated genes, called virtual-knockout perturbed genes, which are used to assess the impact of the gene knockout and reveal the gene’s function in the analyzed cells.

Last updated 2 months ago

functional-genomicsgene-functiongene-knockoutgene-regulatory-networkvirtual-knockout-experiments

4.85 score 43 stars 11 scripts 251 downloads

rPanglaoDB - Download and Merge Single-Cell RNA-Seq Data from the PanglaoDB Database

Download and merge labeled single-cell RNA-seq data from the PanglaoDB <https://panglaodb.se/> into a Seurat object.

Last updated 2 years ago

data-integrationdata-miningrna-seqsingle-cellsingle-cell-rna-seq

4.41 score 26 stars 20 scripts 193 downloads

retriever - Generate Disease-Specific Response Signatures from the LINCS-L1000 Data

Generates disease-specific drug-response profiles that are independent of time, concentration, and cell-line. Based on the cell lines used as surrogates, the returned profiles represent the unique transcriptional changes induced by a compound in a given disease.

Last updated 3 years ago

2.22 score 11 scripts 180 downloads

SCORPION - Single Cell Oriented Reconstruction of PANDA Individual Optimized Networks

Constructs gene regulatory networks from single-cell gene expression data using the PANDA (Passing Attributes between Networks for Data Assimilation) algorithm.

Last updated 9 months ago

1.00 score 8 scripts 523 downloads