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Materials for Analyzing Next-Generation Sequencing (ANGUS) course.

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.github
 
 
.idea
.idea
 
 
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admin
admin
 
 
figures
figures
 
 
files
files
 
 
for-instructors
for-instructors
 
 
jetstream
jetstream
 
 
rob_map
rob_map
 
 
rob_quant
rob_quant
 
 
.DS_Store
.DS_Store
 
 
.ftpconfig
.ftpconfig
 
 
.gitignore
.gitignore
 
 
00_intro_organization.rst
00_intro_organization.rst
 
 
01_Download_and_test.rst
01_Download_and_test.rst
 
 
02_working_with_archives.rst
02_working_with_archives.rst
 
 
03_the_filesystem.rst
03_the_filesystem.rst
 
 
04_DataFilesAndScripts.rst
04_DataFilesAndScripts.rst
 
 
ChIP-Seq-Ensembl.png
ChIP-Seq-Ensembl.png
 
 
ChandlerDeSeq.rst
ChandlerDeSeq.rst
 
 
DeSeq2_Salmon_Tutorial.md
DeSeq2_Salmon_Tutorial.md
 
 
GATK_pipeline.md
GATK_pipeline.md
 
 
GWAS.md
GWAS.md
 
 
GenomicsShell.rst
GenomicsShell.rst
 
 
IntroductionControlFlowR.md
IntroductionControlFlowR.md
 
 
IntroductionControlFlowR.rst
IntroductionControlFlowR.rst
 
 
Jupyter-Notebook-Notes.md
Jupyter-Notebook-Notes.md
 
 
Jupyter-is-fun.ipynb
Jupyter-is-fun.ipynb
 
 
JupyterEmptyNotebook.png
JupyterEmptyNotebook.png
 
 
JupyterFilesList.png
JupyterFilesList.png
 
 
JupyterNotebookCommandAndText.png
JupyterNotebookCommandAndText.png
 
 
JupyterNotebookFirstCommand.png
JupyterNotebookFirstCommand.png
 
 
JupyterNotebookGraphics.png
JupyterNotebookGraphics.png
 
 
JupyterNotebookMultipleKernels.png
JupyterNotebookMultipleKernels.png
 
 
LC-github.rst
LC-github.rst
 
 
MacManesTrimming.rst
MacManesTrimming.rst
 
 
MacManes_AssemblyQuest.rst
MacManes_AssemblyQuest.rst
 
 
MacManes_BUSCO.rst
MacManes_BUSCO.rst
 
 
MacManes_MapQuest.rst
MacManes_MapQuest.rst
 
 
MacManes_Trinity.rst
MacManes_Trinity.rst
 
 
MacManes_UNIX.rst
MacManes_UNIX.rst
 
 
MacManes_adventure_week1.rst
MacManes_adventure_week1.rst
 
 
MacManes_adventure_week2.rst
MacManes_adventure_week2.rst
 
 
MacManes_kallisto.rst
MacManes_kallisto.rst
 
 
Makefile
Makefile
 
 
README.md
README.md
 
 
R_Introductory_tutorial_2015.md
R_Introductory_tutorial_2015.md
 
 
Read_&_munge_NGS_tutorial.R
Read_&_munge_NGS_tutorial.R
 
 
Read_group_info.md
Read_group_info.md
 
 
Rintro.rst
Rintro.rst
 
 
SOAPdeNovoTrans_count_eXpress.rst
SOAPdeNovoTrans_count_eXpress.rst
 
 
analyzing_drosophila_htseq.rst
analyzing_drosophila_htseq.rst
 
 
analyzing_nanopore_data.md
analyzing_nanopore_data.md
 
 
analyzing_nanopore_data_Loman.rst
analyzing_nanopore_data_Loman.rst
 
 
arabidopsis_assembly_challenge.rst
arabidopsis_assembly_challenge.rst
 
 
assembling-ecoli.rst
assembling-ecoli.rst
 
 
assembly-trinity.md
assembly-trinity.md
 
 
automation-2.md
automation-2.md
 
 
bcl2fastq.rst
bcl2fastq.rst
 
 
chip-seq.md
chip-seq.md
 
 
code-of-conduct.rst
code-of-conduct.rst
 
 
command-line-and-rstudio.md
command-line-and-rstudio.md
 
 
conf.py
conf.py
 
 
counting.md
counting.md
 
 
dammit_annotation.md
dammit_annotation.md
 
 
database_resources.md
database_resources.md
 
 
day1.rst
day1.rst
 
 
day2.rst
day2.rst
 
 
densityCurves.R
densityCurves.R
 
 
deseq2-asthma.md
deseq2-asthma.md
 
 
drosophila_htseq.R
drosophila_htseq.R
 
 
drosophila_rnaseq1.rst
drosophila_rnaseq1.rst
 
 
drosophila_rnaseq_bwa_htseq.rst
drosophila_rnaseq_bwa_htseq.rst
 
 
drosophila_rnaseq_counting_htseq.rst
drosophila_rnaseq_counting_htseq.rst
 
 
eel-pond.rst
eel-pond.rst
 
 
filezila-file-transfer.md
filezila-file-transfer.md
 
 
functional_annotation.rst
functional_annotation.rst
 
 
functional_annotation_2016.rst
functional_annotation_2016.rst
 
 
genome-assembly.md
genome-assembly.md
 
 
genome-comparison-and-phylogeny.rst
genome-comparison-and-phylogeny.rst
 
 
genome_tophat_htseq_counts.zip
genome_tophat_htseq_counts.zip
 
 
git-koans.rst
git-koans.rst
 
 
github.md
github.md
 
 
howe-mgrast.rst
howe-mgrast.rst
 
 
howe-ncbi.rst
howe-ncbi.rst
 
 
index.md
index.md
 
 
instructors-guide.rst
instructors-guide.rst
 
 
interval-analysis-and-visualization.rst
interval-analysis-and-visualization.rst
 
 
introduction-to-R-and-dataframes.md
introduction-to-R-and-dataframes.md
 
 
introduction-to-automation.md
introduction-to-automation.md
 
 
jupyter_notebook.rst
jupyter_notebook.rst
 
 
killifish_lengths.txt
killifish_lengths.txt
 
 
kmers-and-sourmash.md
kmers-and-sourmash.md
 
 
kmers-etc.rst
kmers-etc.rst
 
 
kraken_species_identification.rst
kraken_species_identification.rst
 
 
linuxbrew_install.rst
linuxbrew_install.rst
 
 
live-coding-test.txt
live-coding-test.txt
 
 
long-and-short-reads.md
long-and-short-reads.md
 
 
long-read.rst
long-read.rst
 
 

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