Search Results for "rna"
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Showing 291 open source projects for "rna"
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kallisto
Near-optimal RNA-Seq quantification
kallisto is a program for near-optimal quantification of transcript abundances from RNA-Seq data, or more generally of target sequences using high-throughput sequencing reads. It is based on the idea of using pseudoalignment to quickly determine reads and targets’ compatibility, with no need for alignment. According to benchmarks done on a Mac desktop computer, kallisto can quantify 30 million human bulk RNA-seq reads in less than 3 minutes with just the read sequences and a transcriptome index, that in itself can take more than 10 minutes to build. ... -
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awesome-single-cell
Community-curated list of software packages and data resources
Community-curated list of software packages and data resources for single-cell, including RNA-seq, ATAC-seq, etc. List of software packages (and the people developing these methods) for single-cell data analysis, including RNA-seq, ATAC-seq, etc. Rapid, accurate and memory-frugal preprocessing of single-cell and single-nucleus RNA-seq data. Find bimodal, unimodal, and multimodal features in your data. Ascend is an R package comprised of fast, streamlined analysis functions optimized to address the statistical challenges of single cell RNA-seq. ... -
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RSeQC
RNA-seq data QC
RSeQC provides a number of functions to evaluate the quality of RNA-seq data. http://rseqc.sourceforge.net/ -
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harmonypy
Integrate multiple high-dimensional datasets with fuzzy k-means
...Harmony is a general-purpose R package with an efficient algorithm for integrating multiple data sets. It is especially useful for large single-cell datasets such as single-cell RNA-seq. -
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Bowtie 2
A fast and sensitive gapped read aligner
...The tool builds compact FM-index-based reference indexes, keeping memory usage low even for large genomes like the human genome. Bowtie 2 outputs alignments in SAM format and includes companion utilities for building and inspecting indexes. It is widely used in bioinformatics pipelines for RNA-seq, DNA-seq, metagenomics, variant analysis, and other sequencing-based research tasks. Overall, Bowtie 2 remains a foundational command-line tool for high-throughput sequence alignment and reproducible computational biology workflows. -
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Subread
High-performance read alignment, quantification and mutation discovery
...It includes Subread aligner, Subjunc exon-exon junction detector and featureCounts read summarization program. Subread aligner can be used to align both gDNA-seq and RNA-seq reads. Subjunc aligner was specified designed for the detection of exon-exon junction. For the mapping of RNA-seq reads, Subread performs local alignments and Subjunc performs global alignments. Subread and Subjunc were published in the following paper: Yang Liao, Gordon K Smyth and Wei Shi. "The Subread aligner: fast, accurate and scalable read mapping by seed-and-vote", Nucleic Acids Research, 2013, 41(10):e108 -
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IsoQuant
Transcript discovery and quantification with long RNA reads
IsoQuant is a tool for the genome-based analysis of long RNA reads, such as PacBio or Oxford Nanopores. IsoQuant allows reconstructing and quantifying transcript models with high precision and decent recall. If the reference annotation is given, IsoQuant also assigns reads to the annotated isoforms based on their intron and exon structure. IsoQuant further performs annotated gene, isoform, exon, and intron quantification. -
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miRge3
Comprehensive analysis of small RNA sequencing data
An update to Python package to perform comprehensive analysis of small RNA sequencing data, including miRNA annotation, A-to-I editing, novel miRNA detection, isomiR analysis, visualization through IGV, processing Unique Molecular Identifieres (UMI), tRF detection and producing interactive graphical output. miRge3.0 is developed in python v3.8 and is a recent update of our previous version miRge2.0. This build includes command line interface (CLI) and cross-platform Graphical User Interface (GUI). ... -
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This Shiny app provides a user-friendly interface for performing Weighted Gene Co-expression Network Analysis (WGCNA) on RNA-seq/Microarray and DNA methylation (Array/Sequencing) data. It allows for data upload, parameter customization, visualization of results, and exporting of analysis outputs. Online webserver https://shinywgcna.serve.scilifelab.se/app/shinywgcna PLEASE NOTE Datasets with larger dimensions (e.g., 1000x100) may fail on the server,because it is only running on 1GB RAM allocation. ...
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rna-test
script for variant calling of RNA-Seq
rna_test.sh is a shell script to run GATK best practice for variant-calling in RNAseq. It uses STAR2.5 for alignment, HaplotypeCaller to call variants, and Annovar to annotate. It also employs STAR-Fusion, Cufflinks and Stringtie FPKM, HTSeq_count and BAM-readcount. Notice: STAR_gene_read and HTSeq_count are added. exac03nontcga is added. STAR-Fusion is added. Stringtie is added. Disable BQSR (-skb) opteion is added. New avsnp(150) is updated. use -dcov in SplitNCigarReads... -
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UniversalMer2
A CLI k-mer counting tool for multiple size of k at once.
UniversalMer is a k-mer counting tool for multiple size of k at once. It is available for DNA, RNA, and protein sequences. The program counts and summarizes the exact frequency of all k-mers from 1-mer to a user-defined maximum length (kmax). This kmax can be specified as any length or can be automatically determined by the longest repeated patterns found in the input sequence. -
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UniversalMer
A CLI k-mer counting tool for multiple sizes of k at once.
UniversalMer is a k-mer counting tool for multiple size of k at once. It is available for DNA, RNA, and protein sequences. The program counts and summarizes the exact frequency of all k-mers from 1-mer to a user-defined maximum length (kmax). Analyzing the k-mer spectrum across multiple values of k can be done in seconds. This program is designed for bioinformatics researchers and scientists. -
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BBMap
BBMap short read aligner, and other bioinformatic tools.
...It is written in pure Java, can run on any platform, and has no dependencies other than Java being installed (compiled for Java 6 and higher). All tools are efficient and multithreaded. BBMap: Short read aligner for DNA and RNA-seq data. Capable of handling arbitrarily large genomes with millions of scaffolds. Handles Illumina, PacBio, 454, and other reads; very high sensitivity and tolerant of errors and numerous large indels. Very fast. BBNorm: Kmer-based error-correction and normalization tool. Dedupe: Simplifies assemblies by removing duplicate or contained subsequences that share a target percent identity. ... -
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MEDe-KIT
Micro Educational and Development Kit (MEDe-KIT)
Micro Educational and Development Kit (MEDe-KIT) is an educational software for storing and viewing information about study material information uploaded to it like images and text descriptions. It uses ODBC for storing uploaded data into local database. Its features also include a genes sequencer for generating combination of DNA and RNA sequence entered. Thanks and hope this is useful for everyone who are interested in science and learning. The project was developed using NetBeans IDE and Java. Default login user name : user Default login password : user -
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oxDNA
A code primarily aimed at DNA and RNA coarse-grained simulations
The oxDNA code has been moved to https://github.com/lorenzo-rovigatti/oxDNA, please go there for new releases. -
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relax
Molecular dynamics by NMR data analysis
The software package 'relax' is designed for the study of molecular dynamics through the analysis of experimental NMR data. Organic molecules, proteins, RNA, DNA, sugars, and other biomolecules are all supported. It supports exponential curve fitting for the calculation of the R1 and R2 relaxation rates, calculation of the NOE, reduced spectral density mapping, the Lipari and Szabo model-free analysis, study of domain motions via the N-state model and frame order dynamics theories using anisotropic NMR parameters such as RDCs and PCSs, the investigation of stereochemistry in dynamic ensembles, and the analysis of relaxation dispersion data. -
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MAF
Bash Framework to combine many preprocessing and alignment tools
DNA and RNA nucleotide sequences are an ubiquitous element of all biological cells and are serving on one hand as a comprehensive library of capabilities for the cells and on the other as an impressive regulatory system to control cellular function. The presented multi-alignment framework (MAF) should give researchers a simple sequence alignment platform as a functional template, flexible enough to adjust all steps but also comprehensive enough to join many different tools and custom parameter combinations if in-depth analysis is necessary or advised in e.g. low read rate situations. ... -
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Gemi
PCR primers / probes design from multiple & degenerate sequences
Gemi, an automated, fast, and easy-to-use bioinformatics tool with a user-friendly interface to design primers and probes for polymerase chain reaction (PCR). Gemi accepts multiple aligned and long DNA and RNA sequences with degenerate nucleotide (non-A/C/G/T bases). Gemi can be used for quantitative, real-time and conventional PCR (qPCR, rt-PCR, etc.), and Sanger sequencing. Gemi can parse large dataset of sequences efficiently. Python source code is available upon request. Milestone: The tool reached about 3000 downloads sine 2012. ... -
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PLEKv2
PLEKv2: predicting lncRNAs and mRNAs
PLEKv2: predicting lncRNAs and mRNAs based on intrinsic sequence features and the Coding-Net model INSTALLATION ------------- We upgraded PLEK to PLEKv2. All you need is RNA sequences (fasta file). Steps: 1. Download PLEK.2.1.tar.gz from * and decompress it. $ tar zvxf PLEK.2.1.tar.gz 2. Compile PLEK2.1 $ cd PLEK2.1 3. decompress Coding_Net_kmer6_orf.h5.bz2 model $ bunzip2 Coding_Net_kmer6_orf.h5.bz2 4. decompress Coding_Net_kmer6_orf_Arabidopsis.h5.bz2 model $ bunzip2 Coding_Net_kmer6_orf_Arabidopsis.h5.bz2 USAGE Python PLEK2.py -i fasta_file -m model(ve: vertebrate , pl: plant) Examples: $ python PLEK2.py -i test.fasta -m ve Aimin Li, Haotian Zhou, Siqi Xiong, Junhuai Li, Saurav Mallik, Rong Fei, Yajun Liu, Hongfang Zhou, Xiaofan Wang, Xinhong Hei, Lei Wang. ... -
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miRDeep*
MiRDeep*
Please cite: An, J., Lai, J., Lehman, M.L. and Nelson, C.C. (2013) miRDeep*: an integrated application tool for miRNA identification from RNA sequencing data. Nucleic Acids Res, 41, 727-737. We will create index for you if you tell us your interested species (j.an@qut.edu.au). download command line version "MDS_command_line_Vxx.zip" clicking "Browse All Files" please find miRPlant in sourceforge for plant miRNA prediction. -
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CTK
CLIP Tool Kit (CTK)
CTK (CLIP Tool Kit) is a computational biology toolkit implemented in Perl, designed for analyzing CLIP sequencing data. It offers a streamlined pipeline from raw reads through peak calling and motif discovery. -
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TileCreator
A soft for designing primers for overlapping tiles over a transcript.
... - Only accepts DNA sequences as input ("T", not "U"). - It does not check for primer specificity nor primer dimers. - It is based on the original olaygo.py script found in seismic-rna by Matthew F. Allan (please check the Rouskin Lab repository). -
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CPAT
RNA coding potential assessment tool
Using RNA-seq, tens of thousands of novel transcripts and isoforms have been identified (Djebali, et al Nature, 2012 , Carbili et al, Gene & Development, 2011) The discovery of these hidden transcriptome rejuvenate the need of distinguishing coding and noncoding RNA. However, Most previous coding potential prediction methods heavily rely on alignment, either pairwise alignment to search for protein evidence or multiple alignments to calculate phylogenetic conservation score (such as CPC , PhyloCSF and RNACode ). ... -
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Weinberg-R2R
Faster creation of aesthetic RNA secondary structure diagrams
R2R is a program to assist in aesthetic drawings of RNA secondary structures. It is primarily aimed at drawing consensus diagrams, but can also draw single RNA molecules. R2R is freely available under the GNU Public License, and runs as a command-line program under UNIX-like systems such as Linux, MacOS Darwin or Cygwin on Windows. R2R was written by Zasha Weinberg. If you use it, please cite this paper: http://bmcbioinformatics.biomedcentral.com/articles/10.1186/1471-2105-12-3 -
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BioBytes PairSync
A Bioinformatics Tool for Basic Information Retrieval
This GUI app allows users to input biological sequences, either manually or by loading from a file. It supports DNA, RNA, and Protein sequences. Users can retrieve various information about the input sequence, such as nucleotide or amino acid frequency, GC content, reverse complement, transcription, translation, amino acid molecular weight, isoelectric point, and open reading frames. Users can save the output information to a text file and clear the output section for a clean slate. ...
