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NextGen Sequencing Analysis

Sequence Analysis

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	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	168	ngs-cookbook-august2018.pdf	Ngs Cookbook August2018		5.09 MB	2018-08-29
Introduction to Next Generation Sequencing Analysis	202	ngs-cookbook-nov2018.pdf	Ngs Cookbook Nov2018		5.11 MB	2018-11-27
Introduction to Next Generation Sequencing Analysis	7	Overview of NGS Analysis.pdf	Overview Of NGS Analysis	Birds-eye overview	3.07 MB	2018-08-29
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	167	rnaseq-august2018-hes.pdf	Rnaseq August2018 Hes		19.49 MB	2018-08-29
Introduction to Next Generation Sequencing Analysis	203	rnaseq-nov2018-hes.pptx	Rnaseq Nov2018 Hes		6.32 MB	2018-11-27
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-jan2019.pdf	Bioinformatics for Beginners - Cookbook - January 2019	PDF of the cookbook with hands-on exercises	7.98 MB	2019-01-17
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	struct_biol_2_15_18.pdf	Introduction to Computational Structural Biology	Presentation on concepts and methods in computational structural biology	13.29 MB	2018-03-01
Bioinformatics for Beginners	18	IntroPhylo_Feb2018.pdf	Introduction to Phylogenetic Analysis	Concepts in building and analysing phylogenetic trees	10.99 MB	2018-03-01
Bioinformatics for Beginners	17	IntroSeqAlign_Feb2018.pdf	Introduction to Sequence Alignment	Sequence alignment concepts	15.30 MB	2018-03-01
Bioinformatics for Beginners	1	omics-overview.pdf	Omics Overview	Omics overview presented at the Bioinformatics for Beginners training.	1.93 MB	2018-03-01

Data Integration, Analysis and Visualization

Gallery	ID	Filename	Name	Description	Size	Last modified
Data Integration, Analysis and Visualization	14	bigdata-sources-integration.pdf	Bigdata Sources For Data Integration	Resource presentation	681.31 KB	2018-03-01
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

Variant Analysis

Gallery	ID	Filename	Name	Size	Last modified
Variant Analysis	42	1-variant-calling-overview-July2018.pdf	1 Variant Calling Overview	1.30 MB	2018-07-23
Variant Analysis	145	2-haplotype-somatic-denovo-July2018.pdf	2 Haplotype Somatic Denovo July2018	368.13 KB	2018-07-23
Variant Analysis	150	3-indels-july2018.pdf	3 Indels July2018	54.92 KB	2018-07-23
Variant Analysis	149	4-Somatic-july2018.pdf	4 Somatic July2018	260.38 KB	2018-07-23
Variant Analysis	148	5-SVs-july2018.pdf	5 SVs July2018	187.97 KB	2018-07-23
Variant Analysis	147	6-variant-annotation-July2018.pdf	6 Variant Annotation July2018	131.94 KB	2018-07-23
Variant Analysis	146	7-population-genetics-association-July2018.pdf	7 Population Genetics Association July2018	601.90 KB	2018-07-23
Variant Analysis	151	bwa-pipeline.pdf	Bwa Pipeline	57.28 KB	2018-07-24
Variant Analysis	50	variant-cookbook-july2018_v2.pdf	Variant Cookbook	2.02 MB	2018-07-31
Variant Analysis	43	variant-network.pdf	Variant Network	1.70 MB	2018-03-02
Variant Analysis	156	variant-networks-2018.pdf	Variant Networks 2018	2.63 MB	2018-07-27

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	Filename	Name	Description	Size	Last modified
Advanced RNA-Seq Analysis	76	apa-may2018.pdf	Apa May2018	Hands-on tutorial for analyzing alternative polyadenylation site usage analysis	40.33 KB	2018-05-18
Advanced RNA-Seq Analysis	96	apa-may2018-PPT.pdf	Apa May2018 PPT		1.11 MB	2018-05-19
Advanced RNA-Seq Analysis	184	arnaseq-manual-jan2019.pdf	Arnaseq Manual January 2019		4.37 MB	2019-01-29
Advanced RNA-Seq Analysis	83	Ballgown.docx	Ballgown - tutorial		216.56 KB	2018-05-19
Advanced RNA-Seq Analysis	185	BP_Trinity.pptx	BP Trinity		2.30 MB	2018-09-26
Advanced RNA-Seq Analysis	186	CircRNA_BP.pptx	CircRNA BP		5.07 MB	2018-09-26
Advanced RNA-Seq Analysis	93	CircRNA_BP.pptx	CircRNA PPT		5.07 MB	2018-05-19
Advanced RNA-Seq Analysis	80	circular-rna-may-2018.pdf	Circular Rna May 2018	Hands-on tutorial for identifying and analyzing circular RNAs	48.39 KB	2018-05-18
Advanced RNA-Seq Analysis	187	Fusion_genes.pptx	Fusion Genes - PPT		38.17 MB	2018-09-26
Advanced RNA-Seq Analysis	91	GATK_pipeline.docx	GATK Pipeline - Tutorial		21.69 KB	2018-05-19
Advanced RNA-Seq Analysis	86	Hisat_StringTie_BallGown.pptx	Hisat StringTie BallGown - PPT		3.25 MB	2018-05-19
Advanced RNA-Seq Analysis	85	hisat2.docx	Hisat2 - Tutorial		329.36 KB	2018-05-19
Advanced RNA-Seq Analysis	183	laptop-setup-sept2018.pdf	Laptop Setup Sept2018		904.42 KB	2018-09-25
Advanced RNA-Seq Analysis	79	linux-basics-may2018.pdf	Linux Basics May2018	Hands-on tutorial for Linux Basics	95.74 KB	2018-05-18
Advanced RNA-Seq Analysis	182	Overview of RNA-Seq Analysis.pdf	Overview Of RNA Seq Analysis		2.68 MB	2018-09-25
Advanced RNA-Seq Analysis	84	code.R	R Code	R code	3.62 KB	2018-05-19
Advanced RNA-Seq Analysis	78	ngs-network-may-2018.pdf	RNA-Seq Network May 2018 - Tutorial	Hands-on training material for network based analysis of NGS data.	2.88 MB	2018-05-19
Advanced RNA-Seq Analysis	95	rnaseq-networks-may-2018.pdf	Rnaseq Networks May 2018 - PPT		3.22 MB	2018-05-19
Advanced RNA-Seq Analysis	90	STAR-Fusion.docx	STAR Fusion - Tutorial		16.57 KB	2018-05-19
Advanced RNA-Seq Analysis	81	STAR-Fusion.sh	STAR Fusion Script		456 B	2018-05-19
Advanced RNA-Seq Analysis	87	BP_Trinity.pptx	Trinity - PPT		1,017.45 KB	2018-05-19
Advanced RNA-Seq Analysis	88	Trinity RNAseq.docx	Trinity RNAseq - Tutorial		20.01 KB	2018-05-19
Advanced RNA-Seq Analysis	188	Variant_Calling.pptx	Variant Calling - PPT		7.20 MB	2018-09-26
Advanced RNA-Seq Analysis	82	Vcall.sh	Variant calling - script		4.16 KB	2018-05-19
Advanced RNA-Seq Analysis	77	viral-may2018.pdf	Viral May2018	Hands-on tutorial for viral integration analysis	61.33 KB	2018-05-18
Advanced RNA-Seq Analysis	189	virus-integration.pptx	Virus Integration		655.54 KB	2018-09-26
Advanced RNA-Seq Analysis	94	virus-integration.pptx	Virus Integration - PPT		170.50 KB	2018-05-19

Computational Drug Design and Discovery

Gallery	ID	Filename	Name	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-nov2018.pdf	Drug Design Manual Nov2018	16.08 MB	2018-11-05
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-concepts.pdf	Programming Concepts	623.34 KB	2018-08-07
Programming for Biomedical Researchers	164	programming-cookbook.pdf	Programming Cookbook	2.53 MB	2018-08-07

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