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NextGen Sequencing Analysis

Sequence Analysis

Visualizing 3D structures as holograms - Using MergeCube

Presentations and Hands-on Training Materials

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Introduction to Next Generation Sequencing Analysis

Gallery	ID	Filename	Name	Description	Size	Last modified
Introduction to Next Generation Sequencing Analysis	5	chipseq-peaks-to-motifs-august-2018.pdf	Chipseq - Peaks To Motifs	Concepts presentation	5.56 MB	2018-08-29
Introduction to Next Generation Sequencing Analysis	8	laptop-setup-august-2018.pdf	Cloud Setup	Setup overview presentation	2.25 MB	2018-08-29
Introduction to Next Generation Sequencing Analysis	3	faes-ngs-network-vijay.pdf	Cytoscape for Network based Analysis of RNA-Seq data	Hands-on exercise cookbook	4.68 MB	2018-03-01
Introduction to Next Generation Sequencing Analysis	224	dnaseq_feb2019.pptx	Dnaseq Presentation Feb2019		6.96 MB	2019-05-13
Introduction to Next Generation Sequencing Analysis	223	dnaseq.sh	dnaseq.sh workflow script - may 2019		4.49 KB	2019-05-13
Introduction to Next Generation Sequencing Analysis	15	v3.8_workshop_CH.pdf	Introduction to Variant Analysis	Basic concepts, methods, hands-on commands	7.48 MB	2018-03-01
Introduction to Next Generation Sequencing Analysis	6	ngs-networks-august-2018.pdf	Network Analysis of Integrated NGS Data	Presentation concepts	3.89 MB	2018-08-29
Introduction to Next Generation Sequencing Analysis	202	ngs-cookbook-may2019.pdf	Ngs Cookbook May 2019		6.15 MB	2019-05-13
Introduction to Next Generation Sequencing Analysis	7	NGS_intro_feb2019.pptx	Overview Of NGS Analysis	Birds-eye overview	4.00 MB	2019-05-13
Introduction to Next Generation Sequencing Analysis	10	RNA-seq lecture-demo-final-020718-clean.pdf	RNA Seq Lecture Demo Final 020718 Clean	RNA-Seq basic concepts, demos, presentation	2.66 MB	2018-03-01
Introduction to Next Generation Sequencing Analysis	227	rnaseq-code.R	Rnaseq - ballgown - r script - May 2019		4.22 KB	2019-05-13
Introduction to Next Generation Sequencing Analysis	203	rnaseq_feb2019.pptx	Rnaseq presentation - Feb 2019		5.75 MB	2019-05-13
Introduction to Next Generation Sequencing Analysis	226	rnaseq.sh	rnaseq.sh workflow script - May 2019		2.33 KB	2019-05-13
Introduction to Next Generation Sequencing Analysis	16	variant-analysis-commands.sh	Shell Script - Commands for Variant Analysis	Shell script with commands used for the variant analysis part of the NGS training.	9.15 KB	2018-08-29
Introduction to Next Generation Sequencing Analysis	9	unix.pdf	Unix	Unix basics, concepts	4.24 MB	2018-03-01

Bioinformatics for Beginners

Gallery	ID	Filename	Name	Description	Size	Last modified
Bioinformatics for Beginners	175	bioinformatics-oct2019.pdf	Bioinformatics for Beginners - Cookbook - October 2019	PDF of the cookbook with hands-on exercises	8.34 MB	2019-10-03
Bioinformatics for Beginners	2	bioinformatics-in-a-box.pdf	Bioinformatics In A Box	A broad bird-eye-view presentation on the field of bioinformatics	292.23 KB	2018-03-01
Bioinformatics for Beginners	19	protein_structure_pred_10_2_19.pptx.pdf	Introduction to Computational Structural Biology	Presentation on concepts and methods in computational structural biology	2.01 MB	2019-10-03
Bioinformatics for Beginners	1	omics-overview.pdf	Omics Overview	Omics overview presented at the Bioinformatics for Beginners training.	1.93 MB	2018-03-01
Bioinformatics for Beginners	248	unix_10_2_19.pptx.pdf	Unix		2.47 MB	2019-10-03

Data Integration, Analysis and Visualization

Gallery	ID	Filename	Name	Description	Size	Last modified
Data Integration, Analysis and Visualization	11	linux-basics-integration.pdf	Linux Basics		1.89 MB	2018-03-01
Data Integration, Analysis and Visualization	12	large-graph-integration.pdf	Graph Based Integration and Analysis of Biological Data - Overview	Presentation concepts	5.10 MB	2018-03-01
Data Integration, Analysis and Visualization	13	data-integration-manual-dec2018.pdf	Data Cleaning Integration - Cookbook	Hands-on training material - cookbook	5.77 MB	2018-12-11
Data Integration, Analysis and Visualization	14	bigdata-sources-integration.pdf	Bigdata Sources For Data Integration	Resource presentation	681.31 KB	2018-03-01

Variant Analysis

Gallery	ID	Filename	Name	Size	Last modified
Variant Analysis	42	1-variant-calling-overview-apr2019.pdf	1 Variant Calling Overview	2.78 MB	2019-04-16
Variant Analysis	145	2-haplotype-somatic-denovo-apr2019.pdf	2 Haplotype Somatic Denovo	1.10 MB	2019-04-16
Variant Analysis	150	3-indels-apr2019.pdf	3 Indels	89.10 KB	2019-04-16
Variant Analysis	149	4-Somatic-apr2019.pdf	4 Somatic	328.08 KB	2019-04-16
Variant Analysis	148	5-CNV and SV-apr2019.pdf	5 CNV and SVs	1.73 MB	2019-04-16
Variant Analysis	147	6-variant-annotation-apr2019.pdf	6 Variant Annotation	856.47 KB	2019-04-16
Variant Analysis	146	7-population-genetics-association-apr2019.pdf	7 Population Genetics Association	601.86 KB	2019-04-16
Variant Analysis	151	bwa-pipeline.pdf	Bwa Pipeline	57.28 KB	2018-07-24
Variant Analysis	220	Calling variants using GATK (Hands-on).pptx	Calling Variants Using GATK (Hands On)	83.21 KB	2019-04-16
Variant Analysis	221	Germline Variant Calling.pdf	Germline Variant Calling	257.66 KB	2019-04-16
Variant Analysis	50	variant-cookbook-apr2019.pdf	Variant Cookbook	2.24 MB	2019-04-16
Variant Analysis	156	variant-networks-2019.pdf	Variant Networks	2.63 MB	2019-04-16

R Plots and Graphs

Gallery	ID	Filename	Name	Description	Size	Last modified
R Plots and Graphs	56	myplots.zip	BioTech76.zip Feb 2019	Contains all scripts and example data used for the R Graphs and Plots course at NIH	12.17 MB	2019-02-12
R Plots and Graphs	194	networks-oct-2018.pdf	Networks Oct 2018		4.06 MB	2018-10-05
R Plots and Graphs	193	plots-manual-feb2019.pdf	Plots Manual Feb 2019		8.05 MB	2019-02-12

Molecular Modeling and Molecular Dynamics

Gallery	ID	Filename	Name	Description	Size	Last modified
Molecular Modeling and Molecular Dynamics	137	abinitio.tar.gz	Abinitio.tar		3.76 MB	2018-07-05
Molecular Modeling and Molecular Dynamics	59	modeling-dynamics-nov2018.pdf	Hands-on exercises manual	This PDF file consists of all the hands-on exercises used for the NIH molecular modeling and dynamics class.	4.93 MB	2018-12-04
Molecular Modeling and Molecular Dynamics	138	md_tut.tar.gz	Md Tut.tar		2.03 MB	2018-07-05
Molecular Modeling and Molecular Dynamics	133	md_faes_2018-mike.z01	md_faes_2018-mike.z01		50.00 MB	2018-07-05
Molecular Modeling and Molecular Dynamics	132	md_faes_2018-mike.z02	md_faes_2018-mike.z02		50.00 MB	2018-07-05
Molecular Modeling and Molecular Dynamics	131	md_faes_2018-mike.z03	md_faes_2018-mike.z03		50.00 MB	2018-07-05
Molecular Modeling and Molecular Dynamics	134	md_faes_2018-mike.zip	md_faes_2018-mike.zip	main part of the 4 part split zip file. download all the four and unzip this main file to extract the complete presentation file.	49.50 MB	2018-07-05
Molecular Modeling and Molecular Dynamics	139	modeller-ex.tar.gz	Modeller Ex.tar		329.37 KB	2018-07-05
Molecular Modeling and Molecular Dynamics	129	tues-mike.pptx	Tues Mike		10.53 MB	2018-07-05
Molecular Modeling and Molecular Dynamics	136	vmd.zip	vmd.zip		26.74 MB	2018-07-05
Molecular Modeling and Molecular Dynamics	130	wed-mike.pptx	Wed Mike		27.28 MB	2018-07-05

Advanced RNA-Seq Analysis

Gallery		ID	T	Filename	Name	Description	Size	Last modified
Advanced RNA-Seq Analysis		245		PPTs.zip	PPTs.zip		9.45 MB	2019-10-03
Advanced RNA-Seq Analysis		246		Scripts.zip	Scripts.zip		10.74 KB	2019-10-03

Computational Drug Design and Discovery

Gallery	ID	Filename	Name	Description	Size	Last modified
Computational Drug Design and Discovery	178	2.docx	2 - ragul files		210.95 KB	2018-09-14
Computational Drug Design and Discovery	177	3.docx	3 - ragul files		2.46 MB	2018-09-14
Computational Drug Design and Discovery	179	4.pdf	4 - ragul files		3.08 MB	2018-09-14
Computational Drug Design and Discovery	181	adt1.pdf	Adt1 - ragul files		952.93 KB	2018-09-14
Computational Drug Design and Discovery	180	adt2.pdf	Adt2 - ragul files		2.18 MB	2018-09-14
Computational Drug Design and Discovery	100	CoMFA theory.pdf	CoMFA Theory		398.39 KB	2018-05-28
Computational Drug Design and Discovery	196	database.mol2	database.mol2		440.14 KB	2018-11-08
Computational Drug Design and Discovery	195	drug-design-manual-april2019.pdf	Drug Design Manual April 2019	April 2019 version	16.91 MB	2019-04-09
Computational Drug Design and Discovery	102	drug_design2018.pdf	Drug Design2018		880.89 KB	2018-05-28
Computational Drug Design and Discovery	98	drug-unix-basics-exercise.pdf	Drug Unix Basics Exercise		83.48 KB	2018-05-28
Computational Drug Design and Discovery	103	ligand-based-exercises.pdf	Ligand Based Exercises		4.46 MB	2018-05-28
Computational Drug Design and Discovery	101	ligand_design.pdf	Ligand Design		3.59 MB	2018-05-28
Computational Drug Design and Discovery	99	ligand1.pdf	Ligand1		477.97 KB	2018-05-28
Computational Drug Design and Discovery	176	ligand1.docx	Ligand1		542.36 KB	2018-09-14
Computational Drug Design and Discovery	104	Ligand2.pdf	Ligand2		154.69 KB	2018-05-29
Computational Drug Design and Discovery	105	Ligand3.pdf	Ligand3		1.43 MB	2018-05-29
Computational Drug Design and Discovery	197	pharmacophore_gist.mol2	pharmacophore_gist.mol2		23.79 KB	2018-11-08
Computational Drug Design and Discovery	198	reference.mol2	reference.mol2		4.23 KB	2018-11-08
Computational Drug Design and Discovery	199	skeleton_active_range.sdf	skeleton_active_range.sdf		56.25 KB	2018-11-08
Computational Drug Design and Discovery	200	tr_p_act.txt	tr_p_act.txt		229 B	2018-11-08
Computational Drug Design and Discovery	201	TrainingSet.zip	TrainingSet.zip		30.12 KB	2018-11-08

Metagenomics Data Analysis

Gallery	ID	Filename	Name	Size	Last modified
Metagenomics Data Analysis	113	2017_metagenomics.pptx	2017 Metagenomics	3.60 MB	2018-06-05
Metagenomics Data Analysis	122	a5assembly-exercise-handout.pdf	A5assembly Exercise Handout	67.47 KB	2018-06-05
Metagenomics Data Analysis	112	humann2.pdf	Humann2	470.63 KB	2018-06-05
Metagenomics Data Analysis	121	krona-exercise-handout.pdf	Krona Exercise Handout	176.12 KB	2018-06-05
Metagenomics Data Analysis	114	lefse.pdf	Lefse	53.51 KB	2018-06-05
Metagenomics Data Analysis	115	megan-exercise-handout.pdf	Megan Exercise Handout	1,003.79 KB	2018-06-05
Metagenomics Data Analysis	116	metaphlan2.pdf	Metaphlan2	55.68 KB	2018-06-05
Metagenomics Data Analysis	117	network-metagenomics.pdf	Network Metagenomics	3.21 MB	2018-06-05
Metagenomics Data Analysis	118	networks-metagenomics-handson.pdf	Networks Metagenomics Handson	2.09 MB	2018-06-05
Metagenomics Data Analysis	111	phyloseq.pdf	Phyloseq	177.32 KB	2018-06-05
Metagenomics Data Analysis	110	phyloseq.Rmd.txt	Phyloseq.Rmd	3.18 KB	2018-06-05
Metagenomics Data Analysis	109	picrust.pdf	Picrust	88.84 KB	2018-06-05
Metagenomics Data Analysis	119	Tuesday_exercise_123_handouts.html	Tuesday Exercise 123 Handouts	260.77 KB	2018-06-05
Metagenomics Data Analysis	120	unix-basics.pdf	Unix Basics	132.46 KB	2018-06-05

Programming for Biomedical Researchers

Gallery	ID	Filename	Name	Size	Last modified
Programming for Biomedical Researchers	159	00_Intro_Python_Programming.pptx	00 Intro Python Programming	6.68 MB	2018-08-07
Programming for Biomedical Researchers	160	01_how_to_run_python_code.ipynb	01 How To Run Python Code	8.16 KB	2018-08-07
Programming for Biomedical Researchers	161	02_intro_python.ipynb	02 Intro Python	27.85 KB	2018-08-07
Programming for Biomedical Researchers	162	03_python_data_analysis.ipynb	03 Python Data Analysis	61.80 KB	2018-08-07
Programming for Biomedical Researchers	163	programming.pdf	Programming Concepts	623.48 KB	2019-08-19
Programming for Biomedical Researchers	164	programming-august2019.pdf	Programming Cookbook - August 2019	5.05 MB	2019-08-19

Statistics Using R

Gallery		ID	T	Filename	Name	Description	Size	Last modified
Statistics Using R		233		statistics-r-cookbook.pdf	Statistics R Cookbook		1.86 MB	2019-09-06

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