Search Results for "rna-seq" - Page 3
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Showing 428 open source projects for "rna-seq"
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SKUDONET ADC, operates at the application layer, efficiently distributing network load and application load across multiple servers. This not only enhances the performance of your application but also ensures that your web servers can handle more traffic seamlessly.
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ChIP-BIT2
ChIP-BIT2 detects weak binding sites of TFs or HMs.
Different from traditional peak callers that detect strong peaks only, ChIP-BIT2 detects both strong and weak peaks from enhancer regions, promoter regions or the whole genome using a pair of sample and input ChIP-seq experiments. It can automatically detect both narrow and wide peaks so can be applied to detecting transcription factor binding events or histone modifications without specific settings. ChIP-BIT2 is an extended version of the ChIP-BIT method: a method designed mainly... -
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A script to filter exome-seq by 1000G, ExAc, dbSNP with minimal coverage and T/N ratio. The script uses the files produced by exome_test.sh. An error is corrected. The script also produces MAF file that only includes variants detected by BOTH GATK and Varscan. A few errors are corrected.
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cnvkit.sh
A short script to run cnvkit
cnvkit.sh is a shell script to run CNVkit for exome-seq. The shell uses the files produced by exome_test.sh. It allows for recentering the baseline by the average log2ratio of a certain chromosome. ***Update*** The seg can be annotated by cytoband with multithreading. Individual chromosomal scattergrams are plotted. -
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Contiki-BBS
Contiki BBS is a tiny, little and text based bulletin board system
Contiki BBS is a tiny, little and text based bulletin board system (BBS) server for the Commodore 64 homecomputer and a compatible ethernet cartridge (e.g. RRnet, 64NIC+). It will also run in a VICE emulator with ethernet support enabled. The BBS itself can be accessed through a standard telnet connection. Despite a floppy disk drive and the ethernet cartridge no further addon hardware is required (for emulation use VICE with ethernet support). -
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seqz.sh
script to run sequenza
seqz.sh is a shell script to run sequenza for exome-seq. The shell uses the files produced by exome_test.sh. *** Update *** The script now allows for multi-threading. The seg can be annoated by cytoband with multithreading. -
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QuiclickRNAseq
An integrated pipeline for RNA-seq analysis
Quiclick is a python framework for RNA-seq data analysis, including data trimming, mapping, counting and RNA editing analysis. -
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Harmony Data Integration
Fast, sensitive and accurate integration of single-cell data
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. Harmony has been tested on R versions =4. Please consult the DESCRIPTION file for more details on required R packages. Harmony has been tested on Linux, OS X, and Windows platforms. -
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APAtrap
Identification of APA sites from RNA-seq data
APAtrap - a tool for identification of APA sites from RNA-seq data. [1] APAtrap user manual Please visit the Wiki page of this website. [2] APAtrap Q&A For Q&A, please visit the Blog page of this website. [3] APAtrap bug report You can report a bug as a Ticket request, or start a topic session in the Discussion webpage of this website. [4] How to cite APAtrap? Ye C, Long Y, Ji G, Li Q. Q, Wu X (2018) APAtrap: identification and quantification of alternative polyadenylation sites... -
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DAMIAN
Identification of pathogenic microorganisms in diagnostic samples
DAMIAN provides capabilities to detect known and novel pathogens in RNA and DNA samples of various sources. It integrates all required processing steps, ranging from the quality control of sequencing reads to the generation of comprehensive reports. The method works for any host organism. -
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MATS is a computational tool to detect differential alternative splicing events from RNA-Seq data. The statistical model of MATS calculates the P-value and false discovery rate that the difference in the isoform ratio of a gene between two conditions exceeds a given user-defined threshold. From the RNA-Seq data, MATS can automatically detect and analyze alternative splicing events corresponding to all major types of alternative splicing patterns. MATS handles replicate RNA-Seq data from both...
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COHCAP
City of Hope CpG Island Analysis Pipeline
COHCAP (City of Hope CpG Island Analysis Pipeline, pronounced "co-cap") is an algorithm to analyze single-nucleotide resolution methylation data (Illumina 450k methylation array, targeted BS-Seq, etc.). Please note: 1) The SourceForge version of COHCAP is no longer being updated. Please see the GitHub version: https://github.com/cwarden45/COHCAP This was the source repository for the Bioconductor version, with some changes after the decision to only provide the code through GitHub. 2... -
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GapFiller
A de novo local assembler for paired reads
GapFiller is a seed-and-extend local assembler to fill the gap within paired reads. It can be used for both DNA and RNA and it has been tested on Illumina data. GapFiller can be used whenever a sequence is to be assembled starting from reads lying on its ends, provided a loose estimate of sequence length. -
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RecNN
Reinforced Recommendation toolkit built around pytorch 1.7
This is my school project. It focuses on Reinforcement Learning for personalized news recommendation. The main distinction is that it tries to solve online off-policy learning with dynamically generated item embeddings. I want to create a library with SOTA algorithms for reinforcement learning recommendation, providing the level of abstraction you like. -
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HyLiTE
Hybrid Lineage Transcriptome Explorer
HyLiTE (Hybrid Lineage Transcriptome Explorer) analyzes high-throughput transcriptome data from allopolyploid species. Allopolyploidy describes the formation of a new hybrid organism from the union of two or more different parents. Allopolyploid species carry multiple copies of each gene (homeologs), which often exhibit unusual expression patterns. Homeolog expression levels can technically be determined from next generation sequencing data (RNA-seq), but in practice, assigning reads to one... -
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epidaurus
tumor epigenetic database
Epidaurus is a collection of epigenetic datasets including transcription factor ChIP-seq, histone ChIP-seq, DNase-seq, FAIRE-seq, DNA methylation, etc. It also includes commonly used genome features (GC content, conservation) and RNA-seq. A user friendly interface has been developed to interrogate and visuzlize these datasets. -
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CusVarDB
CusVarDB generated variant protein database from NGS-datasets
CusVarDB is a windows based tool for creating a variant protein database from Next-generation sequencing datasets. The program supports variant calling for Genome, RNA-Seq and ExomeSeq datasets. The program performs mainly 4 modules 1. Align the datasets with reference database 2. Perform the variant calling using Genome Analysis Toolkit (GATK) 3. Annotate the variant using ANNOVAR 4. Create the variant protein database Apart from the main modules, the program also supports additional... -
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WellMeth
Genome-Wide DNA Methylation Analysis with RRBS
WellMeth is a integrated framework for Reduced Representation Bisulfite-Seq analysis -
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seqdiva
SeqDivA:Sequence Diversity Analysis
Sequence Diversity Analysis - SeqDivA version 1.0 is a python-based tool with a friendly GUI designed for Linux and Mac OS. Utility: Run alignment algorithms (water, needle, and blast) to compare all-vs.-all protein, DNA, and RNA sequences. SeqDivA provides similarity, identity, and bit-score matrixes and dot plots to explore/illustrate the diversity (homology degree) of the sequences, enabling the delimitation of the twilight zone. Installation: - Download SeqDivA - decompress... -
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TI2BioP allows mainly the calculation of topological indices (spectral moments) derived from inferred and artificial 2D structures of DNA, RNA and proteins being possible to carry out a structure-function correlation irrespective of sequence alignments. TI2BioP version 3.0 is a python platform with a graphical interface designed for Windows, Linux and Mac OS.
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pyrus-seq
Pyrus analyzes paired-end whole genome sequencing data
Pyrus analyzes paired-end and non-paired-end whole genome sequencing data. The program is designed to identify and statistically weight potential chromosomal rearrangements identified in the data using parameters derived from the dataset itself. -
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MetaAnnotator
Fast and Accurate Taxonomic Annotation for Metagenomic reads
Hi everyone. NCBI has adopted a new format for its ref sequences. MetaAnnotator currently can not work on latest version of NCBI ref seq. I will update the program soon. You can use the archive version ftp://ftp.ncbi.nlm.nih.gov/genomes/archive/old_refseq/Bacteria/all.fna.tar.gz before that. Taxonomic annotation is a critical first step for analysis of metagenomic data. Despite a lot of tools being developed, the performance (both running time and accuracy) is still not satisfactory... -
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svdetect.sh is a shell script to run SVDetect to detect SV in exome-seq and Shatterproof to detect chromothripsis. ***Update*** The output files of SVDetect can be annotated by genes with multi-threading.
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rRNAFinder
Fast ribosomal RNA detector and annotator
rRNAFinder is a small perl software package, which can be used to automatically predict and classify the ribosome RNA genes using the assembled genome/metagenome contigs as input. The software were only tested on the Linux operating system. "rRNAFinder.pl" program included in the package uses nhmmer program searching against the arc.hmm, bac.hmm, and euk.hmm databases to identify rRNA genes from the input contigs. The predicated rRNA genes include 16S, 18S, 23S, 28S, 5S, and 5.8S rRNA genes...