Categories
Tag: GAM
Diversity of Unusual Ribosomal Genes and Ecological Origin of Rice ( Oryza spp.)
Author Listed: Xiyu Tan (College of Life Science, South China Agricultural University, Guangzhou 510642, China) Guixiang Peng (College of Natural Resources and Environment, South China Agricultural University, Guangzhou 510642, China) Sajid Muhammad (College of Agriculture and Biotechnology, Zhejiang University, Hangzhou 310023, China) Sidra Kaleem (Riphah Institute of Pharmaceutical Sciences, Islamabad…
Endogenous Coriobacteriaceae enriched by a high-fat diet promotes colorectal tumorigenesis through the CPT1A-ERK axis
Bacteria Strain Cori.ST1911 was isolated from fresh stool of 20-week-old C57/BL6J mice fed a HFD at the Animal Center of the West China Hospital of Sichuan University. Briefly, faecal particles were ground with a glass grinding rod and suspended in sterile phosphate-buffered saline (PBS). After gradient dilution, the suspension was…
All-Time Highs Provide An Opportunity To Trim Long Equity Exposure
Dzmitry Skazau/iStock via Getty Images By Andrew Prochnow Typically observed around this time of the year, the Santa Claus rally has propelled the stock market upward in the final month. Recently, the Dow Jones Industrial Average achieved a new record high, with the S&P 500 and Nasdaq not far behind….
Retrieving NM:i edit distance field in .sam files generated by vg giraffe and vg surject
Retrieving NM:i edit distance field in .sam files generated by vg giraffe and vg surject 0 Hello, I’m trying to compare alignment results between mapping tools, however, I’ve noticed that the .sam files I’ve made using vg surject are missing the NM:i field. Is there a way to generate a…
ggplot2 – Alpha gradient for geom_spline in R
I have a large and complex dataframe. I wish to fit a smoothed line. (loess isn’t possible due to large data and gam doesn’t look good). I have found geom_spline or stat_spline from the ggforumla package to work well. I wish to adjust the transparency of the spline line based…
KEGG T01028: 701915
Entry 701915 CDS T01028 Symbol KRT25 Name (RefSeq) keratin, type I cytoskeletal 25 KO K07604 type I keratin, acidic Organism mcc Macaca mulatta (rhesus monkey) Pathway mcc04915 Estrogen signaling pathway mcc05150 Staphylococcus aureus infection Brite KEGG Orthology (KO) [BR:mcc00001] 09150 Organismal Systems 09152 Endocrine system 04915 Estrogen signaling pathway 701915 (KRT25) 09160 Human Diseases 09171 Infectious disease: bacterial 05150 Staphylococcus…
Can I use vg tools to calculate the depth for a bed range file like with samtools depth?
Can I use vg tools to calculate the depth for a bed range file like with samtools depth? 0 Hi, I have some gam files produce by vg call and I want to know the mean/min/max depth for some ranges stored in a bed file. I could surject the gam…
Lack of correspondance of GFA node IDs to giraffe/call node IDs
I have a GFA graph built with PGGB using several samples. I want to genotype some other samples with short reads using VG Giraffe. After investigating how to generate the corresponding indexes for VG Giraffe from a GFA generated with PGGB, I think I have found a way to do…
Split complementation of base editors to minimize off-target edits
Komor, A. C., Kim, Y. B., Packer, M. S., Zuris, J. A. & Liu, D. R. Programmable editing of a target base in genomic DNA without double-stranded DNA cleavage. Nature 533, 420–424 (2016). Article CAS PubMed PubMed Central Google Scholar Nishida, K. et al. Targeted nucleotide editing using hybrid prokaryotic…
HiFi read alignment with vg giraffe
HiFi read alignment with vg giraffe 0 Hi, I used vg giraffe to align long read hifi sequences to a pangenome using vg giraffe and these are the numbers i am getting by running vg stats. Total alignments: 4144653 Total primary: 4144653 Total secondary: 0 Total aligned: 4144644 Total perfect:…
Researchers explore immunomodulating targets for improving glioblastoma therapies
In a recent article published in EMBO Molecular Medicine, researchers investigated cellular, molecular, and spatiotemporal heterogeneity of glioblastoma (GBM), a malignant and highly aggressive primary brain tumor. Study: Single-cell profiling and zebrafish avatars reveal LGALS1 as immunomodulating target in glioblastoma. Image Credit: Triff/Shutterstock.com They performed single-cell ribonucleic acid sequencing (scRNA-seq) of…
Assembloid CRISPR screens reveal impact of disease genes in human neurodevelopment
Culture of hiPS cells The hiPS cell lines used in this study were validated as previously described51. The SEC61B-mEGFP hiPS cell line (AICS-0059 cl.36) was developed at the Allen Institute for Cell Science (www.allencell.org/cell-catalog.html) and is distributed through Coriell43. The CAG::Cas9 cell line was genetically engineered in the laboratory (the…
Bug of vg surject
Bug of vg surject 0 Hello I tried to use vg surject to convert gam to bam, there was a problem here. If i generate the bam from giraffe by parameter ‘-o bam’, the size of bam file is more bigger than bam generated from vg surject. And then, using…
Commonly collected thermal performance data can inform species distributions in a data-limited invader
Animal collection and housing Ten chameleons were captured from an established non-native population in Central Florida from October 2019-February 2020 (N = 7 males, 2 females) and October 2020 (N = 1 male). Adult panther chameleons were housed individually in an experimental mesh exclosure at the US Department of Agriculture (USDA), Wildlife Services, National…
r – Add Ggplot Output to in Nested For Loop
I have this nested for loop where for each site and species combination it runs a GAM model on count vs time (n ~ s(unix)). I am struggling to get the ggplot outputs to save in the final list. Currently it only overwrites the last site and species combination. The…
Problem generating scatterplot with ggplot and tidyverse – tidyverse
Hi technocrat. I did what you told me, library(tidyverse)data<- read.csv(“who_data.csv”)reduced <- data[complete.cases(data),]head (reduced)reduced ggplot(reduced, aes(x = Year, y = Life.expectancy)) +geom_point() + scale_y_continuous(limits=c(30,100))+geom_smooth() ggplot(reduced, aes(x = Year, y = BMI)) +geom_point() + scale_y_continuous(limits=c(0,100))+geom_smooth() ggplot(reduced, aes(x = Year, y = Schooling)) +geom_point() + scale_y_continuous(limits=c(0,25))+geom_smooth() Now, I only has a line saying…
r – Group option in ggplot
I get an error in the group option: ! Problem while computing aesthetics. ℹ Error occurred in the 2nd layer. Caused by error in check_aesthetics(): ! Aesthetics must be either length 1 or the same as the data (30) ✖ Fix the following mappings: group test=structure(list(pay = c(1.65041035963578, 1.52885759360691, 1.5477592978624,…
Gene Editing Tools Based on CRISPR/Cas System and Their Improvement Strategies
Gene Editing Tools Based on CRISPR/Cas System and Their Improvement Strategies XIN Yuan1,TIAN Kai-ren3,QIAO Jian-jun1,2,3,CAIYIN Qing-ge-le1,2,**() 1 School of…
Kenya: IPC Food Security & Malnutrition Snapshot – Acute Food Insecurity: July 2023 – January 2024; Acute Malnutrition: April – October 2023 – Kenya
Attachments Acute Food Insecurity Overview Between July and September 2023, coinciding with the Agropastoral harvest and pastoral lean season, about 2.8 million people in Kenya’s Arid and Semi-Arid Lands (ASALs) are classified in IPC Phase 3 or above (Crisis or worse). Among them 2.3 million are experiencing Crisis, IPC Phase…
Kenya: IPC Acute Food Insecurity and Acute Malnutrition Analysis (July 2023 – January 2024) Published on 1 September 2023 – Kenya
Attachments Overview From July to September 2023 (coinciding with the harvest season for Agropastoral livelihoods and the lean season for pastoral livelihoods), approximately 2.8 million people (17 percent of the ASAL population) are classified in IPC Acute Food Insecurity (AFI) Phase 3 or above (Crisis or worse) of these 2.3…
problem in BIOMOD2
hi, can anyone explain this section, please # myBiomodModelOut <- BIOMOD_Modeling( myBiomodData, models = c('GLM', 'GAM', 'RF', 'SRE', 'MAXENT.Phillips'), models.options = myBiomodOption, NbRunEval=3, DataSplit=70, Prevalence=0.5, VarImport=3, models.eval.meth = c('TSS','ROC'), SaveObj = TRUE, rescal.all.models = TRUE, do.full.models = FALSE, modeling.id = paste('Fagus orientalis',"FirstModeling",sep="")) I tried to train with this scrip that…
Using vg gamsort with naive sorting algorithm
Hello, I am currently using VG to map reads to a graph I made (using a HPC), and I’m having issues when sorting the ouput gam: vg gamsort \ -p \ ${filename}_mapped.gam > ${filename}_mapped.sorted.gam break into sorted chunks [ ] 0.0%^M break into sorted chunks [= ] 1.1%^M break into…
VG mapping paired-end reads: error [xg]: multiple hits for XXX
Hi everyone, I did create my first graph using vcf from HGDP as follow: vg construct -r ref.fa -v sub-chrXX.vcf.gz > pXX.vg vg ids -j $(for i in $(seq 1 22); do echo p${i}.vg; done) vg index -x all.xg $(for i in $(seq 1 22); do echo p${i}.vg; done) vg…
VG node not present in graph
Hello everyone, I’m currently working on constructing my first pangenome using VG and could use some help. My approach involves using VCF files from individuals in HGDP and following the steps outlined on their GitHub tutorial: GitHub Tutorial Link. This tutorial fits my needs but wasn’t updated since 2020 …..
display vcf after giraffe alignment on IGV
display vcf after giraffe alignment on IGV 0 I performed Giraffe alignment to map reads to the HPRC pangenome, resulting in a gam file. Subsequently, I utilized the following commands to generate a .vcf file: Generated a pack file with the following command: ./vg pack –x hprc-v1.0-mc-grch38-minaf.0.1.gbz –g hprc1004mapped.gam >…
A genome-wide association study of blood cell morphology identifies cellular proteins implicated in disease aetiology
INTERVAL study The INTERVAL study was a randomised trial of approximately 45,000 blood donors aged eighteen years or older who were recruited at 25 NHSBT (National Health Service Blood and Transplant) static donor centres across England21. The study was approved by the Cambridge East Research Ethics Committee and we complied…
The number of SVs called by `vg call` is much smaller than the number of SVs in the VCF used to construct the graph
The number of SVs called by `vg call` is much smaller than the number of SVs in the VCF used to construct the graph 0 My objective is to identify the structural variations (SVs) located on chromosome NC_058090.1. The reason for solely focusing on a single chromosome is due to…
US Bancorp DE Increases Ownership Stake in WNS (Holdings) Limited: A Vote of Confidence in Growth and Profitability
US Bancorp DE, a financial institution, has increased its ownership stake in WNS (Holdings) Limited by 6.2% during the first quarter of the year. This information was disclosed in their recent Form 13F filing with the Securities and Exchange Commission (SEC). At the end of the reporting period, US Bancorp…
creating vcf file after giraffe alignment
creating vcf file after giraffe alignment 0 I am using the HPRC human pangenome as a reference for aligning my whole genome sequencing data. My focus is on the HLA region, and I anticipate improved alignment results using the pangenome reference. To achieve this, I make use of the provided…
Question with manipulating OD gene list when running PCA
Hello, I am using Seurat 4.9.9.905 and Pagoda2 1.0.10 to do sc clustering on an integrated object. I integrated two merged sample sets with var features and normalization applied to each of the two merged objects. I would like to do the clustering in Pagoda. This is my integration script:…
why does vg convert doesn’t work?
why does vg convert doesn’t work? 1 I am using vg version 1.49.0 on Ubuntu I am trying to convert a gam file to a gfa format and it is not working. I have the file hprc1004mapped.gam and I run the command: ./vg convert –G hprc1004mapped.gam > hprc1004mapped.gfa And I…
Nextflow files not referenced correctly when using wildcard in a for loop
Hi, I’m having some problems with my nextflow workflow when I use wildcards (*) to call in files. The files are created fine, (using process augment below) but when it is used by process snarls, it calls them as follows: CH-A2504_1.aug.gam -> workdir/2c/ce66a6417872a428111b7c2a5995d4/CH-A2504_01.aug.gam CH-A2504_1.aug.pg -> workdir/2c/ce66a6417872a428111b7c2a5995d4/CH-A2504_01.aug.pg … … CH-A2504_23.aug.gam ->…
How to address the heteroskedasticity and non-normality of my residuals in my model? – General
My study is about the influence of board diversity (gender and age) and fund size on the voting behavior of pension funds. I have also included control variables that concern the board type, board size, fund type, and also control for time. This is only a snippet, but I have…
A Study on Graph Centrality Measures of Different Diseases Due to DNA Sequencing
Author Listed: Ghulam Muhiuddin (Department of Mathematics, Faculty of Science, University of Tabuk, Tabuk 71491, Saudi Arabia) Sovan Samanta (Department of Mathematics, Tamralipta Mahavidyalaya, West Bengal 721636, India) Abdulrahman F. Aljohani (Department of Mathematics, Faculty of Science, University of Tabuk, Tabuk 71491, Saudi ArabiaDepartment of Mathematical Sciences, George Mason University,…
Decreased left heart flow in fetal lambs causes left heart hypoplasia and pro-fibrotic tissue remodeling
Coil implantation in fetal lambs We have complied with all relevant ethical regulations for animal testing. All procedures followed the Canadian Council on Animal Care guidelines and were approved by the University of Western Ontario Council on Animal Care (protocol 2010-257). Time-dated pregnant Dorset × Rideau Arcott ewes (gestational age 76 days,…
Substantial reduction in read mapping following VG surject
Substantial reduction in read mapping following VG surject 0 I did a small comparison of total mapping of a small short-read dataset to: a graph constructed using cactus-minigraph composed of eight whole genome alignments using VG giraffe the same cactus-minigraph graph, but indexed using VG and mapped to with VG…
vg giraffe unavailable perf events issue
vg giraffe unavailable perf events issue 0 Hi, I’m trying to map WGS reads to genome graph using vg giraffe. And I got a warning related to “perf events” while mapping reads. Can I ignore this warning? Here is the log for my execution. Preparing Indexes Loading Minimizer Index Loading…
population-level stratagy of vg call
population-level stratagy of vg call 0 Hello VG Team, I have been contemplating whether there is a more efficient approach to perform population-level Structural Variants (SVs) calling using the VG calling pipeline. Based on my understanding, the VG calling pipeline consists of the following steps: 1) vg construct to create…
vg map time consuming
vg map time consuming 1 Hi vg team, The vg map command has been running for 4 days. Initially, the size of the .gam file accumulated to around 100G, but then suddenly dropped to 1G. Currently, the size is around 2.3G and it continues to increase. The command used is…
Uganda – Karamoja, IPC Acute Malnutrition Analysis, February 2023 – January 2024 (Issued June 15, 2023) – Uganda
Attachments Overview Over 89,000 children aged 6 to 59 months and 10,000 pregnant or lactating women (PLW) are expected to suffer from acute malnutrition in the Karamoja region of Uganda between February 2023 and January 2024. Of the nine districts in Karamoja, during the onset of high acute malnutrition (February…
Comment: warning[vg::Watchdog]
Thank you for your replay! No error was eventually reported because the command didn’t end up running through. I run this conmand **vg giraffe -t 24 -Z 63-pg.d2.gbz -d 63-pg.d2.dist -m 63-pg.d2.min -f IRIS_313-7684_1.QC.fastq.gz -f IRIS_313-7684_2.QC.fastq.gz > IRIS_313-7684_mapped.gam** When I first started running this command, the size of the **gam**…
Exosomal circRNA: emerging insights into cancer progression and clinical application potential | Journal of Hematology & Oncology
He G, Peng X, Wei S, Yang S, Li X, Huang M, et al. Exosomes in the hypoxic TME: from release, uptake and biofunctions to clinical applications. Mol Cancer. 2022;21:19. Article PubMed PubMed Central Google Scholar Downs-Canner SM, Meier J, Vincent BG, Serody JS. B cell function in the tumor…
Retrieving alignment scores with vg surject
Retrieving alignment scores with vg surject 0 Hello! I’m trying to get multiple alignments with their corresponding alignment scores for paired-end reads against a pangenome using vg giraffe, and then vg surject to convert gam to bam. As result, the generated bam file contains multiple alignments for paired-end reads but…
vg convert does not preserve the order of the reads
vg convert does not preserve the order of the reads 0 When I use vg convert (v.1.39) to convert a gam file to a gaf file (or vice versa), I find that the order of the reads will not be preserved. For example, when I sort the reads according to…
Introducing a New Tool for the Investigation of Complex Genome Interactions
Credit: Julia Fekecs, National Human Genome Research Institute Researchers at the Berlin Institute of Medical Systems Biology of the Max Delbrück Center (MDC-BIMSB) have developed a technique called Genome Architecture Mapping (GAM) allowing the identification of previously invisible genomic connections. Ever since the revelation of its basic structure seventy years…
New tool reveals hidden complexity of genome architecture
A German team of scientists have developed a technique known as Genome Architecture Mapping that allows them to study complex genome interactions. Researchers at the Berlin Institute of Medical Systems Biology of the Max Delbrück Centre (MDC-BIMSB), Germany have developed a technique called Genome Architecture Mapping (GAM) that allows scientists…
New Genome Architecture Mapping Tool to Study Genome Interactions
In a new study appearing in Nature Methods, researchers from the Berlin Institute of Medical Systems Biology at the Max Delbrück Center describe a new technique based on the previously developed Genome Architecture Mapping (GAM) they’ve dubbed multiplex-GAM, which allows investigators to examine new and complex DNA interactions. The authors…
Study finds new tool to study complex genome interactions
Washington [US], June 20 : Researchers uncovered previously unknown information about the genome’s spatial architecture by relying solely on Hi-C, a workhorse tool developed in 2009 to study DNA interactions. The study was published in the journal, ‘Nature Methods.’ “With a black-and-white TV, you can see the shapes but everything…
Introducing a new tool for analyzing intricate genome interactions
Newswise — People who owned black-and-white television sets until the 1980s didn’t know what they were missing until they got a color TV. A similar switch could happen in the world of genomics as researchers at the Berlin Institute of Medical Systems Biology of the Max Delbrück Center (MDC-BIMSB) have…
Scientists develop new technique to peer into the genome’s spatial architecture
People who owned black-and-white television sets until the 1980s didn’t know what they were missing until they got a color TV. A similar switch could happen in the world of genomics as researchers at the Berlin Institute of Medical Systems Biology of the Max Delbrück Center (MDC-BIMSB) have developed a…
Very few snp and indels variation were identified using PAV variation input file base on vg call
Very few snp and indels variation were identified using PAV variation input file base on vg call 0 Hi all, We want to find the snp and indels variation from the result vcf file BS_graph_call.vcf by using the pan_genome vg analysis software. There are only **fewer than 20 snp and…
A pangenome reference of 36 Chinese populations
Populations and samples For Phase I of the CPC project, we selected 68 samples from 731 individuals with genomes deep-sequenced using next-generation sequencing. Following a previous study5, we applied a procedure to quantitatively evaluate the genetic diversity coverage based on principal component analysis results. We selected individuals using a statistic…
What is the node_id in vg giraffe output (gaf or gam)?
What is the node_id in vg giraffe output (gaf or gam)? 0 Hi, I am playing with the genome graph I built from 2 different individual whole genome sequencing data. Also, I generated 1 million simulated reads. However, while I tried to map the simulated read back to the genome…
ggplot2 – How to add a rectangle to a ggplot graph with a logged y-axis without changing the y-axis scale
I am trying to add a rectangle to a ggplot graph with a logged y-axis using annotate() or geom_rect(). The rectangle is bounded by two x-axis values (which are dates) and needs span the enitre y-axis. However, whenever I add the rectangle, it changes the scale of the y-axis. For…
You will be using RStudio to pull the data set and
You will be using RStudio to pull the data set and answer the following questions. Task 1 of 2: You will be using Boston data set to predict per capita crime rate using the other variables in this data set. 1. To begin, load in the Boston data set. The…
Quantitative Synthetic Biology for Biologics Production
Biologics accounted for more new drug approvals than did small molecules for the first time in 2022, marking a significant shift in the pharmaceutical industry (1). Large-molecule pipelines are also moving from standard monoclonal antibodies (MAbs) to more complex and difficult-to-express molecules, which intensifies pressure on the industry to meet…
Application of CRISPR/Cas9-mediated gene editing for abiotic stress management in crop plants
1 Introduction Abiotic stresses such as drought, heat, cold, salt, pesticides, metals and metalloids deteriorate agro-ecological conditions and hence, negatively impact upon agricultural production. The abiotic stress impairs with regular growth and development of plant plants, thus limiting their yield and quality of produce (Boyer, 1982; Pandey et al., 2017). Plants…
r – Combining logaritmic with non-logaritmic data
I want to show the correlation between for example loudness and streams for a spotify dataset. Therefore I want to graph the correlation. The first image is what I get using Spearman for the correlation and for the plot geom_smooth with the gam method: If i make the dataset logaritmic…
Advance on engineering of bacteriophages
Introduction Bacteriophage (phage) is a class of widespread viruses exclusively infecting bacteria, playing a key role in ecosystems.1–3 Since phages were discovered over a hundred years ago, many techniques and reagents, such as DNA polymerase, restriction endonuclease, ligase, and CRISPR/Cas system, have been developed from phages, which have together accelerated…
Recent advances in CRISPR-based genome editing technology and its applications in cardiovascular research | Military Medical Research
Doudna JA, Charpentier E. Genome editing. The new frontier of genome engineering with CRISPR-Cas9. Science. 2014;346(6213):1258096. Article PubMed Google Scholar Doudna JA. The promise and challenge of therapeutic genome editing. Nature. 2020;578(7794):229–36. Article CAS PubMed PubMed Central Google Scholar Nambiar TS, Baudrier L, Billon P, Ciccia A. CRISPR-based genome editing…
Converting gam to gaf
Converting gam to gaf 1 I noticed it is now possible to output alignments in gaf files instead of gam, which is great! How difficult would it be to convert gam to gaf? Gaf is definitely easier to parse than using jq for the json conversion of gam, but I’d…
Speed up vg call ?
Speed up vg call ? 1 Dear all, has anyone found a good way of speeding up vg call by chunking or another method ? Current chunking seems to lead to a very modest speedup of 0-20% so maybe is not the right approach. Specifically, I have aligned with vg…
Genome editing techniques based on bacterial-artificial-chromosome in herpesvirus research
In a recent study published in the Microorganisms journal, researchers in China reviewed the uses of bacterial-artificial-chromosome (BAC)-based genome editing techniques in herpesvirus research. Review: Bacterial-Artificial-Chromosome-Based Genome Editing Methods and the Applications in Herpesvirus Research. Image Credit: Panuwach / Shutterstock Herpesviruses are significant human and animal pathogens. Exploring the role of specific…
Kenya: IPC Acute Food Insecurity and Acute Malnutrition Analysis (February – June 2023) Published on 20 February 2023 – Kenya
Attachments In the current period, February 2023, corresponding to the short rain harvest season, a slight decrease in the severity of food insecurity is observed across Kenya’s ASAL areas, which presented four counties in IPC AFI Phase 4 (Emergency) in the previous season (namely Isiolo, Turkana, Marsabit and Mandera) that…
Human mtDNA Haplogroup Classification Using a Pangenomic Reference Graph
Tool:HaploCart: Human mtDNA Haplogroup Classification Using a Pangenomic Reference Graph 0 Current mitochondrial DNA (mtDNA) haplogroup classification tools map reads to a single reference genome and perform inference based on the detected mutations to this reference. This approach biases haplogroup assignments towards the reference and prohibits accurate calculations of the…
miceforest vs scikit-learn – compare differences and reviews?
What are some alternatives? When comparing miceforest and scikit-learn you can also consider the following projects: Keras – Deep Learning for humans Prophet – Tool for producing high quality forecasts for time series data that has multiple seasonality with linear or non-linear growth. Surprise – A Python scikit for building…
Emerging role of STING signalling in CNS injury: inflammation, autophagy, necroptosis, ferroptosis and pyroptosis | Journal of Neuroinflammation
Langlois JA, Rutland-Brown W, Wald MM. The epidemiology and impact of traumatic brain injury: a brief overview. J Head Trauma Rehabil. 2006;21:375–8. doi.org/10.1097/00001199-200609000-00001. Article PubMed Google Scholar Cao HQ, Dong ED. An update on spinal cord injury research. Neurosci Bull. 2013;29:94–102. doi.org/10.1007/s12264-012-1277-8. Article PubMed Google Scholar O’Donnell MJ, Xavier D,…
Mitogenome-wise codon usage pattern from comparative analysis of the first mitogenome of Blepharipa sp. (Muga uzifly) with other Oestroid flies
Outcome of DNA sequencing, assembly, and validation In this study, initially total DNA was isolated from the finely chopped, full-grown pupa of Blepharipa sp. The NanoDrop spectrophotometer (1294 ng/μl) and the Qubit fluorometer (732.8 ng/μl) both found that the concentration of total DNA in the sample at an optimum level for mitochondrial DNA enrichment. The Tape Station profile showed…
Bioconductor – adaptest
DOI: 10.18129/B9.bioc.adaptest This package is for version 3.11 of Bioconductor; for the stable, up-to-date release version, see adaptest. Data-Adaptive Statistics for High-Dimensional Multiple Testing Bioconductor version: 3.11 Data-adaptive test statistics represent a general methodology for performing multiple hypothesis testing on effects sizes while maintaining honest statistical inference when…
H2O is an in-memory platform for distributed, scalable machine learning
H2O is an in-memory platform for distributed, scalable machine learning. H2O uses familiar interfaces like R, Python, Scala, Java, JSON and the Flow notebook/web interface, and works seamlessly with big data technologies like Hadoop and Spark. H2O provides implementations of many popular algorithms such as Generalized Linear Models (GLM), Gradient…
Merging .gam files
Merging .gam files 1 Can anyone point me towards a method to merge gam files that are created by using ‘ vg map ‘ to map illumina reads to my genome graph? I would like to be able to map all of the sequencing runs separately and then merge the…