Search Results for "epig-seq" - Page 2
Sort By:
Showing 267 open source projects for "epig-seq"
View related business solutions-
MongoDB Atlas runs apps anywhereMongoDB Atlas gives you the freedom to build and run modern applications anywhere—across AWS, Azure, and Google Cloud. With global availability in over 115 regions, Atlas lets you deploy close to your users, meet compliance needs, and scale with confidence across any geography.
-
Build Data Resilience - Take the Assessment TodayIs your recovery strategy as strong as you think? Take this quick self-assessment to check your recovery readiness and gain tailored insights. In only 2 minutes, you'll learn where you fall on the recovery readiness scale.
-
1
Piping Server
Infinitely transfer between every device over pure HTTP with pipes
...The first one waits for the other. The most important thing is that the data are streamed. This means that you can transfer any data infinitely. The demo below transfers an infinite text stream with seq inf. You can transfer any kind of data infinitely on a stream. Streams are very efficient in terms of both time and space. All you need is to have either a Web browser or curl, which are widely pre-installed. You do not need to install any extra software. -
2
CPT
CPT: A Pre-Trained Unbalanced Transformer
...Token embeddings found in the old checkpoints are copied. And other newly added parameters are randomly initialized. We further train the new CPT & Chinese BART 50K steps with batch size 2048, max-seq-length 1024, peak learning rate 2e-5, and warmup ratio 0.1. Aiming to unify both NLU and NLG tasks, We propose a novel Chinese Pre-trained Un-balanced Transformer (CPT). -
3
OmicSelector
Feature selection and deep learning modeling for omic biomarker study
OmicSelector is an environment, Docker-based web application, and R package for biomarker signature selection (feature selection) from high-throughput experiments and others. It was initially developed for miRNA-seq (small RNA, smRNA-seq; hence the name was miRNAselector), RNA-seq and qPCR, but can be applied for every problem where numeric features should be selected to counteract overfitting of the models. Using our tool, you can choose features, like miRNAs, with the most significant diagnostic potential (based on the results of miRNA-seq, for validation in qPCR experiments). -
4
Fusion Detection Pipeline
Fusion gene detection pipeline bundled into a Singularity container.
Fusion gene detection by RNA-seq requires prior setup of several software modules and dependencies which might be troublesome. Furthermore, fusion detection tools tend to report many false positives. Therefore, we developed a detection and filtering workflow bundled into a Singularity container for a streamlined and easy-to-use application. Arriba and FusionCatcher are utilized for fusion calling. -
Earn up to 16% annual interest with Nexo.Put idle assets to work with competitive interest rates, borrow without selling, and trade with precision. All in one platform. Geographic restrictions, eligibility, and terms apply.
-
5
Cyclops
An advanced platform for writing functional applications in Java 8
Fast purely functional datastructures (Vector, Seq / List, LazySeq / LazyList, NonEmptyList, HashSet, TreeSet, TrieSet, HashMap, LinkedMap, MultiMap, TreeMap, BankersQueue, LazyString, Discrete Interval Encoded Tree, Zipper, Range, Tree, DifferenceList, HList, Dependent Map). Structural Pattern Matching API (deconstruct algebraic product and sum types). Improved type safety via the removal of unsafe APIs -- E.g. -
6
-
7
CStone
Short-read de novo assembler that identifies chimeric contigs.
> CStone wiki: https://sourceforge.net/p/cstone/wiki/Home/ Related Software: 1. CStone: (See wiki) 2. CSReadGen: https://sourceforge.net/projects/csreadgen/ 3. CView: https://sourceforge.net/projects/cview/ 4. ChimSim: https://sourceforge.net/projects/chimsim/ 5. TVScript: https://sourceforge.net/projects/tvscript/ 6. SeQuester: https://sourceforge.net/projects/sequester/ 7. TreeScope: https://sourceforge.net/projects/treescope/ -
8
CSReadGen
RNA-Seq read simulator that offers a wide range of parameter options.
> CSReadGen wiki: https://sourceforge.net/p/csreadgen/wiki/Home/ Related software: 1. CStone: https://sourceforge.net/projects/cstone/ 2. CSReadGen: (See wiki) 3. CView: https://sourceforge.net/projects/cview/ 4. ChimSim: https://sourceforge.net/projects/chimsim/ 5. TVScript: https://sourceforge.net/projects/tvscript/ 6. SeQuester: https://sourceforge.net/projects/sequester/ 7. TreeScope: https://sourceforge.net/projects/treescope/ -
9
scDAPA
Detection and visualization of dynamic alternative polyadenylation
scDAPA - a tool for detection and visualization of dynamic alternative polyadenylation from scRNA-seq data [1] scDAPA user manual Please visit the Wiki page of this website. [2] scDAPA Q&A For Q&A, please visit the Blog page of this website. [3] scDAPA 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 scDAPA? Ye C, Zhou Q, Wu X, Yu C, Saban D.R, Li Q.Q (2020) scDAPA: detection and visualization of dynamic alternative polyadenylation from single cell RNA-seq data. ... -
Build Securely on AWS with Proven FrameworksMoving to the cloud brings new challenges. How can you manage a larger attack surface while ensuring great network performance? Turn to Fortinet’s Tested Reference Architectures, blueprints for designing and securing cloud environments built by cybersecurity experts. Learn more and explore use cases in this white paper.
-
10
miRSim
Seed-based RNA-Seq Simulator
The miRSim tool can generate the synthetic RNA-Seq data in standard fastq/fasta format by utilizing the sequence-specific properties (i.e., seed and xseed (remaining part of the sequence after removing seed)). Additionally, miRSim also generates the ground truth in CSV format that provides information about genomic location, CIGAR string, sequence, and expression counts. -
11
Keras TCN
Keras Temporal Convolutional Network
TCNs exhibit longer memory than recurrent architectures with the same capacity. Performs better than LSTM/GRU on a vast range of tasks (Seq. MNIST, Adding Problem, Copy Memory, Word-level PTB...). Parallelism (convolutional layers), flexible receptive field size (possible to specify how far the model can see), stable gradients (backpropagation through time, vanishing gradients). The usual way is to import the TCN layer and use it inside a Keras model. The receptive field is defined as the maximum number of steps back in time from current sample at time T, that a filter from (block, layer, stack, TCN) can hit (effective history) + 1. ... -
12
exome-test
script for variant calling of Exome-Seq
exome_test.sh is a shell script to run GATK best practice and varscan for variant-calling in exomseq. It uses bwa for alignment, UnifiedGenotyper and varscan to call variants, and Annovar to annotate. It also employs DepthofCoverage and BAM-readcount. [Notice] MAF files compatible with MutSigCV are added. The Annovar filter dbnsfp30a is updated. Correction of an error in the title line of merge file. -ni option added. -vb option (-B in varscan) added exac03nontcga is added. An... -
13
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 for detecting narrow peaks in promoter regions as described in the following paper: Xi Chen et al., "ChIP-BIT: Bayesian inference of target genes using a novel joint probabilistic model of ChIP-seq profiles", Nucleic Acids Res (2016) 44 (7): e65. -
14
OMRuben
Open Music library dealing with various compositional techniques.
...Developed by Ruben Sverre Gjertsen and ported to lisp 2015. Download OM for free here: http://repmus.ircam.fr/openmusic/home Update 3/1-2021: Many bug fixes, rhythmic conversion from multi-seq to poly are now more precise. Demo patches should work, you need to manually select input files on your system. -
15
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.
-
16
FusionCatcher
Somatic fusion-genes finder for RNA-seq data
FusionCatcher searches for novel/known somatic fusion genes, translocations, and chimeras in RNA-seq data (paired-end reads from Illumina NGS platforms like Solexa and HiSeq) from diseased samples. The aims of FusionCatcher are: - very good detection rate for finding candidate fusion genes, - very easy to use (i.e. no a priori knowledge of databases and bioinformatics is needed in order to run FusionCatcher), - very good detection of challenging fusion genes, like for example IGH fusions, CIC fusions, DUX4 fusions, CRLF2 fusions, TCF3 fusions, etc... -
17
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. -
18
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). -
19
APAtrap
Identification of APA sites from RNA-seq data
...Q, Wu X (2018) APAtrap: identification and quantification of alternative polyadenylation sites from RNA-seq data. Bioinformatics 34(11): 1841–1849. https://academic.oup.com/bioinformatics/article/34/11/1841/4816794 -
20
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. -
21
-
22
...MATS handles replicate RNA-Seq data from both paired and unpaired study design. More information can be found at http://rnaseq-mats.sourceforge.net.
-
23
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) In addition to the original NAR paper, please see the following links: Benchmarks: http://www.nature.com/protocolexchange/protocols/2965#/introduction Protocol Exchange Files: http://sourceforge.net/projects/cohcap/files/Protocol_Exchange_Example.zip 3) Custom Annotation Files (including EPIC Array): https://sourceforge.net/projects/cohcap/files/additional_Bioconductor_annotations.zip/download -
24
HyLiTE
Hybrid Lineage Transcriptome Explorer
...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 homeolog over another is extremely challenging, particularly on a whole-genome scale. HyLiTE automates this process, and allows gene expression patterns to be explored even in very complex allopolyploid species. -
25
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.
