R-universe search: sirna

Showing 9 of total 9 results (show query)

tacazares

SeedMatchR:Find Matches to Canonical SiRNA Seeds in Genomic Features

On-target gene knockdown using siRNA ideally results from binding fully complementary regions in mRNA transcripts to induce cleavage. Off-target siRNA gene knockdown can occur through several modes, one being a seed-mediated mechanism mimicking miRNA gene regulation. Seed-mediated off-target effects occur when the ~8 nucleotides at the 5’ end of the guide strand, called a seed region, bind the 3’ untranslated regions of mRNA, causing reduced translation. Experiments using siRNA knockdown paired with RNA-seq can be used to detect siRNA sequences with potential off-target effects driven by the seed region. 'SeedMatchR' provides tools for exploring and detecting potential seed-mediated off-target effects of siRNA in RNA-seq experiments. 'SeedMatchR' is designed to extend current differential expression analysis tools, such as 'DESeq2', by annotating results with predicted seed matches. Using publicly available data, we demonstrate the ability of 'SeedMatchR' to detect cumulative changes in differential gene expression attributed to siRNA seed regions.

Maintained by Tareian Cazares. Last updated 1 years ago.

deseq2-analysis mirna rna-seq sirna transcriptomics

18.9 match 7 stars 4.54 score 7 scripts

bioc

XNAString:Efficient Manipulation of Modified Oligonucleotide Sequences

The XNAString package allows for description of base sequences and associated chemical modifications in a single object. XNAString is able to capture single stranded, as well as double stranded molecules. Chemical modifications are represented as independent strings associated with different features of the molecules (base sequence, sugar sequence, backbone sequence, modifications) and can be read or written to a HELM notation. It also enables secondary structure prediction using RNAfold from ViennaRNA. XNAString is designed to be efficient representation of nucleic-acid based therapeutics, therefore it stores information about target sequences and provides interface for matching and alignment functions from Biostrings and pwalign packages.

Maintained by Marianna Plucinska. Last updated 5 months ago.

sequencematching alignment sequencing genetics cpp

3.7 match 4.18 score 4 scripts

sybig

RPPanalyzer:Reads, Annotates, and Normalizes Reverse Phase Protein Array Data

Reads in sample description and slide description files and annotates the expression values taken from GenePix results files (text file format used by many microarray scanner and software providers). After normalization data can be visualized as boxplot, heatmap or dotplot.

Maintained by Torsten Schoeps. Last updated 1 years ago.

3.3 match 1 stars 3.63 score 71 scripts

bioc

synlet:Hits Selection for Synthetic Lethal RNAi Screen Data

Select hits from synthetic lethal RNAi screen data. For example, there are two identical celllines except one gene is knocked-down in one cellline. The interest is to find genes that lead to stronger lethal effect when they are knocked-down further by siRNA. Quality control and various visualisation tools are implemented. Four different algorithms could be used to pick up the interesting hits. This package is designed based on 384 wells plates, but may apply to other platforms with proper configuration.

Maintained by Chunxuan Shao. Last updated 5 months ago.

immunooncology cellbasedassays qualitycontrol preprocessing visualization featureextraction

3.6 match 3.30 score 2 scripts

bioc

crisprBowtie:Bowtie-based alignment of CRISPR gRNA spacer sequences

Provides a user-friendly interface to map on-targets and off-targets of CRISPR gRNA spacer sequences using bowtie. The alignment is fast, and can be performed using either commonly-used or custom CRISPR nucleases. The alignment can work with any reference or custom genomes. Both DNA- and RNA-targeting nucleases are supported.

Maintained by Jean-Philippe Fortin. Last updated 5 months ago.

crispr functionalgenomics alignment aligner bioconductor bioconductor-package bowtie crispr-analysis crispr-cas9 crispr-design crispr-target grna grna-sequence grna-sequences sgrna sgrna-design

1.2 match 3 stars 5.86 score 7 scripts 4 dependents

mcanouil

insane:INsulin Secretion ANalysEr

A user-friendly interface, using Shiny, to analyse glucose-stimulated insulin secretion (GSIS) assays in pancreatic beta cells or islets. The package allows the user to import several sets of experiments from different spreadsheets and to perform subsequent steps: summarise in a tidy format, visualise data quality and compare experimental conditions without omitting to account for technical confounders such as the date of the experiment or the technician. Together, insane is a comprehensive method that optimises pre-processing and analyses of GSIS experiments in a friendly-user interface. The Shiny App was initially designed for EndoC-betaH1 cell line following method described in Ndiaye et al., 2017 (<doi:10.1016/j.molmet.2017.03.011>).

Maintained by Mickaël Canouil. Last updated 2 months ago.

beta-cells endoc-betah1 insulin-secretion pancreas shiny statistics stats

1.2 match 3 stars 5.48 score 4 scripts

bioc

crisprBwa:BWA-based alignment of CRISPR gRNA spacer sequences

Provides a user-friendly interface to map on-targets and off-targets of CRISPR gRNA spacer sequences using bwa. The alignment is fast, and can be performed using either commonly-used or custom CRISPR nucleases. The alignment can work with any reference or custom genomes. Currently not supported on Windows machines.

Maintained by Jean-Philippe Fortin. Last updated 5 months ago.

crispr functionalgenomics alignment aligner bioconductor bioconductor-package bwa crispr-analysis crispr-cas9 crispr-design crispr-target grna grna-sequence grna-sequences sgrna sgrna-design

1.2 match 1 stars 4.30 score 6 scripts

cogdisreslab

KinaseTauScore:Tau Scores For Human Kinases

This data package provides the tau scores for each kinase based on its activity in Alzheimer's disease samples. The data was generated by using an siRNA Library to knock down individual kinases and then measuring the total Tau protein Expression and the phopho-Tau protein expression. The resulting data wasc reposited online. This package processes the resulting data to create a meaningful Tau Score for each Kinase based on its activity.

Maintained by Ali Sajid Imami. Last updated 3 years ago.

experimentdata proteome expressiondata

0.5 match 2.70 score

junhuili1017

ZetaSuite:Analyze High-Dimensional High-Throughput Dataset and Quality Control Single-Cell RNA-Seq

The advent of genomic technologies has enabled the generation of two-dimensional or even multi-dimensional high-throughput data, e.g., monitoring multiple changes in gene expression in genome-wide siRNA screens across many different cell types (E Robert McDonald 3rd (2017) <doi: 10.1016/j.cell.2017.07.005> and Tsherniak A (2017) <doi: 10.1016/j.cell.2017.06.010>) or single cell transcriptomics under different experimental conditions. We found that simple computational methods based on a single statistical criterion is no longer adequate for analyzing such multi-dimensional data. We herein introduce 'ZetaSuite', a statistical package initially designed to score hits from two-dimensional RNAi screens.We also illustrate a unique utility of 'ZetaSuite' in analyzing single cell transcriptomics to differentiate rare cells from damaged ones (Vento-Tormo R (2018) <doi: 10.1038/s41586-018-0698-6>). In 'ZetaSuite', we have the following steps: QC of input datasets, normalization using Z-transformation, Zeta score calculation and hits selection based on defined Screen Strength.

Maintained by Junhui Li. Last updated 3 years ago.

0.5 match 2.00 score 2 scripts