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Tutorial: Park Test for Heteroskedasticity In R Commander
R Park-Test
updated 6 months ago by 41k • written 5.9 years ago by ▴ 10
0
votes
0
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7.9k
views
Tutorial: Multicollinearity VIF (Variance Inflation Factor) Analysis in Panel data EVIEWS 9
R eviews
updated 6 months ago by 41k • written 5.9 years ago by ▴ 10
23
votes
19
replies
6.4k
views
10 follow
Tutorial: MutScan: Detect important mutations by scanning FastQ files directly
fastq mutation cancer target
updated 8 months ago by 41k • written 7.2 years ago by ★ 2.5k
1
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0
replies
1.4k
views
Tutorial: Fall 2017 Introduction to Human Genomics for Clinical Informaticists
genome
updated 6 months ago by 41k • written 5.9 years ago by ▴ 90
0
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1
reply
1.7k
views
Tutorial: Guide Tutorial DEAP 2.1 In Windows 7
DEAP2.1 R stata
updated 8 months ago by 41k • written 5.9 years ago by ▴ 10
0
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1
reply
1.8k
views
Tutorial: Nonparametric Regression STATA 15
STATA-15 Nonparametric-Regression STATA
updated 6 months ago by 41k • written 5.9 years ago by ▴ 10
3
votes
3
replies
8.4k
views
Tutorial: High Speed Downloading of SRA, SAM and Fastq Files
fastq sam Aspera-Connect sra
updated 6 months ago by 41k • written 6.0 years ago by ▴ 100
2
votes
0
replies
6.7k
views
Tutorial: How to - Install Python packages in a virtual environment (virtualenv)
ubuntu cutadapt virtualenv python windows
updated 6 months ago by 41k • written 6.0 years ago by ▴ 320
0
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0
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2.8k
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Tutorial: Autocorrelation With Breusch Godfrey Serial Correlation LM Test R Commander
LM-Test R Autocorrelation Breusch-Godfrey
updated 6 months ago by 41k • written 6.0 years ago by ▴ 10
0
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0
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3.0k
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Tutorial: Normality Test For JB (Jarque Bera) Test R Commander
Jarque-Bera-Test R-Commander
updated 6 months ago by 41k • written 6.0 years ago by ▴ 10
0
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0
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1.3k
views
Tutorial: Data Panel In R Commander
R
updated 6 months ago by 41k • written 6.0 years ago by ▴ 10
10
votes
1
reply
8.6k
views
Tutorial: How to select reads with specific flag using samtools
next-gen-sequencing
updated 6 months ago by 41k • written 6.3 years ago by ▴ 110
12
votes
1
reply
4.9k
views
Tutorial: RepSeq data processing and analysis
immunology tcr repseq sequencing repertoire
updated 13 months ago by 41k • written 8.3 years ago by 3.5k
1
vote
0
replies
2.0k
views
Tutorial: How to display Agilent CGH array in IGV
IGV CGH
updated 6 months ago by 41k • written 6.0 years ago by ★ 2.4k
3
votes
2
replies
8.4k
views
Tutorial: Use fastp to preprocess FASTQ data with unique molecular identifer (UMI) integrated
FASTQ UMI fastp
updated 6 months ago by 41k • written 6.0 years ago by ★ 2.5k
39
votes
6
replies
19k
views
Tutorial: Creating chromosome karyotype plot with R and ggplot2
ggplot2 R chromosome karyotype
updated 6 months ago by 41k • written 6.3 years ago by ★ 3.4k
15
votes
1
reply
6.8k
views
Tutorial: A compilation of conversion tools for BED, SAM/BAM, psl, pslx, blast tabular and blast xml
psl SAM blast BED
updated 6 months ago by 41k • written 6.1 years ago by ★ 3.0k
5
votes
5
replies
6.7k
views
Tutorial: use firehose_get to download TCGA data
tcga RNA-Seq
updated 6 months ago by 41k • written 6.1 years ago by ▴ 130
7
votes
1
reply
2.2k
views
Tutorial: A gentle introduction to biogo
sequence golang biogo
updated 6 months ago by 41k • written 6.1 years ago by ★ 1.7k
0
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1
reply
3.0k
views
Tutorial: Accessing sequences using batch entrez
genome
updated 6 months ago by 41k • written 6.1 years ago by • 0
42
votes
16
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23k
views
15 follow
Tutorial: Tutorial: Analyze exome Copy number variation (CNV) in single patient or in population.
GISTIC varscan2 CNV copy-number
updated 16 months ago by 41k • written 8.2 years ago by ★ 2.4k
2
votes
0
replies
3.1k
views
Tutorial: use the tool slicer to split big files (like FASTQ) to smaller files for parallel processing
opengene slicer fastq splitter
updated 5 months ago by 41k • written 6.1 years ago by ★ 2.5k
5
votes
2
replies
3.0k
views
Tutorial: Get GC Content from UCSC with perl script (mysql)
myql ucsc gc-content perl
updated 6 months ago by 41k • written 6.6 years ago by ★ 9.3k
5
votes
0
replies
2.1k
views
Tutorial: Installing multiprocessor-capable MEME to work with a Slurm job scheduler environment
slurm meme parallel
updated 6 months ago by 41k • written 6.2 years ago by 35k
9
votes
9
replies
4.0k
views
Tutorial: Determine % of reference genome covered by aligned SAM/BAM
reference-coverage ngs
updated 6 months ago by 41k • written 6.2 years ago by 86k
12
votes
4
replies
2.0k
views
Tutorial: Tutorials for Library Normalization in DESeq2 and EdgeR
EdgeR DESeq2
updated 8 months ago by 41k • written 6.2 years ago by ▴ 590
11
votes
7
replies
14k
views
Tutorial: Removing rows with duplicate values based on 1 or more key values - linux awk
awk linux bash
updated 6 months ago by 41k • written 6.2 years ago by 86k
7
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2
replies
1.8k
views
Tutorial: Introduction to Human Genomics for Clinical Informaticists
genome
updated 6 months ago by 41k • written 6.3 years ago by ▴ 90
4
votes
1
reply
1.8k
views
Tutorial: One of the easy way to achieve read count and RPKM file
RNA-Seq
updated 6 months ago by 41k • written 6.3 years ago by ▴ 40
1
vote
0
replies
1.6k
views
Tutorial: Using Subversion to update /devel branch of Bioconductor package
bioconductor subversion
updated 6 months ago by 41k • written 6.3 years ago by ▴ 350
12
votes
11
replies
7.1k
views
Tutorial: How to upload your RNA-Seq data to NCBI Sequence Read Archive (SRA)
NCBI Bioproject SRA BioSample
updated 7 months ago by 41k • written 6.7 years ago by ★ 2.4k
9
votes
5
replies
2.1k
views
Tutorial: What is new in samtools release 1.5 [Solstice Release] (21st June 2017)
samtools
updated 6 months ago by 41k • written 6.4 years ago by 99k
25
votes
15
replies
8.6k
views
8 follow
Tutorial: Syllabus To Learn Bioinformatics From Online Video Resources
course training mooc
updated 9 months ago by 41k • written 10.9 years ago by 9.7k
54
votes
5
replies
14k
views
6 follow
Tutorial: Machine Learning For Cancer Classification - Part 4 - Plotting A Kaplan-Meier Curve For Survival Analysis
r
updated 14 months ago by 41k • written 10.0 years ago by ★ 1.2k
3
votes
1
reply
2.2k
views
Tutorial: Convert bam files to fastq in numbers as indicated in samtools flagstat stats.
samtools bam alignment fastq sequence
updated 6 months ago by 41k • written 6.5 years ago by ★ 1.6k
6
votes
2
replies
4.0k
views
Tutorial: GATK method for filtering vcf lines using GT values at all or multisample level.
genome vcf genotype variant-filtration
updated 6 months ago by 41k • written 6.5 years ago by ★ 1.6k
2
votes
6
replies
3.0k
views
Tutorial: Rembrandt Glioma Data Analysis (PART I) - Are Gender specific genes related to cancer ?
gene R Rembrandt
updated 8 months ago by 41k • written 7.4 years ago by ▴ 140
7
votes
2
replies
11k
views
Tutorial: Howto use NCBI programs behind a HTTP proxy
blast-plus HTTP-proxy SRA-toolkit
updated 17 months ago by 41k • written 7.8 years ago by ★ 1.8k
11
votes
6
replies
4.8k
views
Tutorial: sharing some naive codes for microarray normalization in R with whom are too new in R alike me
R
updated 16 months ago by 41k • written 7.8 years ago by ★ 4.2k
4
votes
0
replies
2.2k
views
Tutorial: Accurate prediction of active enhancers using PARE
ChIP-Seq histone-modification enhancer
updated 6 months ago by 41k • written 6.6 years ago by ▴ 100
3
votes
2
replies
3.7k
views
Tutorial: Galaxy Tutorial on ChIP-seq
galaxy ChIP-Seq
updated 6 months ago by 41k • written 6.7 years ago by ▴ 30
10
votes
2
replies
3.6k
views
Tutorial: Graph visualization with igraph in R
Visualization igraph Graph R Network
updated 6 months ago by 41k • written 6.7 years ago by 26k
19
votes
2
replies
3.3k
views
Tutorial: Beginner's Handbook to Next Generation Sequencing
NGS
updated 6 months ago by 41k • written 6.7 years ago by ▴ 640
2
votes
3
replies
2.6k
views
Tutorial: It's about the journey, and not the destination
R network
updated 6 months ago by 41k • written 6.7 years ago by ★ 1.2k
17
votes
13
replies
2.0k
views
Tutorial: Screen shots of text (please don't)!
meta
updated 6 months ago by 41k • written 6.7 years ago by 53k
2
votes
3
replies
1.9k
views
Tutorial: Help demonstrate reproducibility in bioinformatics with the GA4GH's tool execution Challenge
GA4GH Docker CWL Rabix
updated 7 months ago by 41k • written 6.8 years ago by ▴ 20
16
votes
6
replies
6.2k
views
Tutorial: How to make your snakefiles self-documenting
snakemake
updated 8 months ago by 41k • written 7.1 years ago by ★ 1.7k
0
votes
2
replies
5.2k
views
Tutorial: Install AMOS on Ubuntu 13.10
sequencing alignment software-error next-gen
updated 2.1 years ago by 41k • written 9.4 years ago by 9.7k
8
votes
2
replies
6.5k
views
Tutorial: Troubleshooting issues with SURPI pipeline for pathogen identification from complex metagenomic NGS data.
metagenomics clinical-genomics
updated 22 months ago by 41k • written 9.1 years ago by 12k
15
votes
2
replies
6.7k
views
Tutorial: Genotype And Snp Calling Review Papers
snp
updated 9 months ago by 41k • written 11.3 years ago by 99k
384 results • Page 5 of 8
Recent Votes
Comment: Annotation Visualization IGV
Comment: Annotation Visualization IGV
Answer: Execute R command on specific termimal
Answer: Where can I get a list of SNPs mapping overlapping genes in humans?
Comment: How do I know how much memory to use when piping to with BBMap suite (OutOfMemor
A: difference between GSEA and Gene Ontology
Answer: Does the Minion demultiplex when basecalling?
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Popular Question to samreen.jasvi • 0
Teacher to h.mon 35k
Scholar to jared.andrews07 ★ 16k
Popular Question to Mr Locuace ▴ 150
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Recent Replies
Comment: Resolving over clustered NGS with Q-scores by sam.himes92 • 0
The system that we used was [Aviti][1]. Our sequencing core was the one who quantified the loading/library concentration. Sorry I don't hav…
Comment: Where can I get a list of SNPs mapping overlapping genes in humans? by Alex Reynolds 35k
I modified the answer with an approach for that use case.
Comment: Where can I get a list of SNPs mapping overlapping genes in humans? by Ram 41k
OP is looking for overlapping genes - genes with presumably different gene IDs that share some loci. I think the `genes.bed` creation logic…
Comment: Where can I get a list of SNPs mapping overlapping genes in humans? by Alex Reynolds 35k
Note: The file `snps.bed` will be very large. You'll need sufficient disk space for this step.
Answer: Where can I get a list of SNPs mapping overlapping genes in humans? by Alex Reynolds 35k
Given files `genes.bed` and `snps.bed`, you could do something like: ``` $ bedmap --echo --echo-map-id --delim '\t' genes.bed snps.bed > a…
Answer: How to add exon annotations to genome annotation by alex.zaccaron ▴ 380
You can use [AGAT][1] to process your annotation file to add the missing exons. I believe `agat_convert_sp_gxf2gxf.pl -g no_exons.gff -o wi…
Comment: Annotation Visualization IGV by Pierre Lindenbaum 158k
and you got answer that should be validate (green tick), or people asked you questions but got no answers.
Comment: Annotation Visualization IGV by awhale01 • 0
Correct I have asked those questions before.
Comment: Annotation Visualization IGV by Pierre Lindenbaum 158k
you asked questions before: review, comment and/or validate them please: https://www.biostars.org/p/9530777/ ; https://www.biostars.org/p/9…
Comment: Ambient RNA removal method that generates whole (integer) counts by EK • 0
Thanks, Jared. Sounds like rounding counts is the simplest approach for now. :)
Comment: Resolving over clustered NGS with Q-scores by Trivas ★ 1.5k
Could you tell us which sequencer you used, how you quantified your library size and concentration, and what your loading concentration was…
Comment: Resolving over clustered NGS with Q-scores by sam.himes92 • 0
I should have mentioned, we ran both Read 1 and 2 well past the points of interest. For each read we ran 75 cycles.
Answer: Resolving over clustered NGS with Q-scores by Trivas ★ 1.5k
It might be because Illumina recommends 26 cycles for Read 1: https://knowledge.illumina.com/instrumentation/general/instrumentation-genera…
Comment: Resolving over clustered NGS with Q-scores by sam.himes92 • 0
Yes at 5%.
Comment: Resolving over clustered NGS with Q-scores by ATpoint 78k
Has phiX been spiked in to increase nucleotide diversity.
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