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Tutorial: PLS SEM (Partial Least Square Sructural Equation Modeling) Analysis WarpPLS 6
R
updated 12 months ago by 43k • written 6.3 years ago by ▴ 10
3
votes
0
replies
2.2k
views
Tutorial: Deep Learning for Cancer Immunotherapy
keras tensorflow
updated 12 months ago by 43k • written 6.3 years ago by 22k
0
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0
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1.6k
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Tutorial: MWD (Mackinnon, White And Davidson) In R
R
updated 12 months ago by 43k • written 6.3 years ago by ▴ 10
0
votes
0
replies
2.2k
views
Tutorial: Transforming (Transformation) Data LN, Log, SQRT In R Commander
R
updated 12 months ago by 43k • written 6.3 years ago by ▴ 10
0
votes
0
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3.7k
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Tutorial: Park Test for Heteroskedasticity In R Commander
R Park-Test
updated 12 months ago by 43k • written 6.3 years ago by ▴ 10
0
votes
0
replies
8.1k
views
Tutorial: Multicollinearity VIF (Variance Inflation Factor) Analysis in Panel data EVIEWS 9
R eviews
updated 12 months ago by 43k • written 6.3 years ago by ▴ 10
1
vote
0
replies
1.5k
views
Tutorial: Fall 2017 Introduction to Human Genomics for Clinical Informaticists
genome
updated 12 months ago by 43k • written 6.3 years ago by ▴ 90
0
votes
1
reply
1.9k
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Tutorial: Nonparametric Regression STATA 15
STATA-15 Nonparametric-Regression STATA
updated 12 months ago by 43k • written 6.4 years ago by ▴ 10
3
votes
3
replies
8.8k
views
Tutorial: High Speed Downloading of SRA, SAM and Fastq Files
fastq sam Aspera-Connect sra
updated 12 months ago by 43k • written 6.4 years ago by ▴ 100
2
votes
0
replies
6.9k
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Tutorial: How to - Install Python packages in a virtual environment (virtualenv)
ubuntu cutadapt virtualenv python windows
updated 12 months ago by 43k • written 6.4 years ago by ▴ 320
0
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0
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2.9k
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Tutorial: Autocorrelation With Breusch Godfrey Serial Correlation LM Test R Commander
LM-Test R Autocorrelation Breusch-Godfrey
updated 12 months ago by 43k • written 6.4 years ago by ▴ 10
0
votes
0
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3.1k
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Tutorial: Normality Test For JB (Jarque Bera) Test R Commander
Jarque-Bera-Test R-Commander
updated 12 months ago by 43k • written 6.4 years ago by ▴ 10
0
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0
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1.4k
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Tutorial: Data Panel In R Commander
R
updated 12 months ago by 43k • written 6.4 years ago by ▴ 10
10
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1
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9.3k
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Tutorial: How to select reads with specific flag using samtools
next-gen-sequencing
updated 12 months ago by 43k • written 6.7 years ago by ▴ 110
2
votes
0
replies
2.1k
views
Tutorial: How to display Agilent CGH array in IGV
IGV CGH
updated 12 months ago by 43k • written 6.4 years ago by ★ 2.4k
3
votes
2
replies
8.9k
views
Tutorial: Use fastp to preprocess FASTQ data with unique molecular identifer (UMI) integrated
FASTQ UMI fastp
updated 12 months ago by 43k • written 6.5 years ago by ★ 2.5k
39
votes
6
replies
20k
views
Tutorial: Creating chromosome karyotype plot with R and ggplot2
ggplot2 R chromosome karyotype
updated 12 months ago by 43k • written 6.7 years ago by ★ 3.5k
15
votes
1
reply
7.2k
views
Tutorial: A compilation of conversion tools for BED, SAM/BAM, psl, pslx, blast tabular and blast xml
psl SAM blast BED
updated 12 months ago by 43k • written 6.5 years ago by ★ 3.0k
6
votes
5
replies
7.0k
views
Tutorial: use firehose_get to download TCGA data
tcga RNA-Seq
updated 12 months ago by 43k • written 6.5 years ago by ▴ 140
7
votes
1
reply
2.3k
views
Tutorial: A gentle introduction to biogo
sequence golang biogo
updated 12 months ago by 43k • written 6.6 years ago by ★ 1.7k
0
votes
1
reply
3.2k
views
Tutorial: Accessing sequences using batch entrez
genome
updated 12 months ago by 43k • written 6.6 years ago by • 0
2
votes
0
replies
3.3k
views
Tutorial: use the tool slicer to split big files (like FASTQ) to smaller files for parallel processing
opengene slicer fastq splitter
updated 11 months ago by 43k • written 6.6 years ago by ★ 2.5k
5
votes
0
replies
2.2k
views
Tutorial: Installing multiprocessor-capable MEME to work with a Slurm job scheduler environment
slurm meme parallel
updated 12 months ago by 43k • written 6.7 years ago by 35k
9
votes
9
replies
4.2k
views
Tutorial: Determine % of reference genome covered by aligned SAM/BAM
reference-coverage ngs
updated 12 months ago by 43k • written 6.7 years ago by 88k
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 12 months ago by 43k • written 6.7 years ago by 88k
7
votes
2
replies
1.9k
views
Tutorial: Introduction to Human Genomics for Clinical Informaticists
genome
updated 12 months ago by 43k • written 6.7 years ago by ▴ 90
4
votes
1
reply
1.9k
views
Tutorial: One of the easy way to achieve read count and RPKM file
RNA-Seq
updated 12 months ago by 43k • written 6.8 years ago by ▴ 40
37
votes
5
replies
6.1k
views
Tutorial: [Beginner] Introduction to bioinformatics file types
fastq fasta bed SAM
updated 8 months ago by ▴ 20 • written 8.8 years ago by ▴ 430
128 results • Page 3 of 3
Recent Votes
The Biostar Handbook. A bioinformatics e-book for beginners.
The Biostar Handbook. A bioinformatics e-book for beginners.
Differential Expression with limma: Contrast and Design Matrix, combinatorial approach valid?
What is Deepvariant default filtering values ?
Answer: Filtering Multi-sample VCF file for all except one Genotype
Answer: Alphaphold 3 pLDDT coloring scheme in chimerax?
Comment: Benchmarking RNASeq Variant Calling Pipeline (Short Reads)
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Comment: Duplicated reads (IDs) from nanopore sequencing by GenoMax 142k
> I get the exact same read with the same ID and all more than once If you have short(er) reads you could be seeing secondary alignments. …
Answer: Duplicated reads (IDs) from nanopore sequencing by marco.barr ▴ 110
Hi, I'm also working with ONT data and with dorado. From experience I tell you that some versions of MInKNOW have bad management of fast5 f…
Comment: Problem with Calling Variants from RNA-Seq data by Esraa • 0
Yes, i specifically ran the RNA-seq best practices, and no i have not taken RNA editing into account considering this is not mentioned in t…
Comment: Problem with Calling Variants from RNA-Seq data by i.sudbery 19k
Have you accounted for A>I RNA editing?
Comment: Problem with Calling Variants from RNA-Seq data by Esraa • 0
**My references** Genome: https://ftp-trace.ncbi.nlm.nih.gov/ReferenceSamples/giab/release/references/GRCh38/GCA_000001405.15_GRCh38_no_al…
Answer: Getting differential ChIP-seq peaks between conditions after calling consensus p by ATpoint 82k
This has formally been investiated by a reputable group here: https://academic.oup.com/nar/article/42/11/e95/1442937 IIRC they think tha…
Comment: RNA seq analysis by Jacek ▴ 10
Thank you so much Matthias this is really helpful, I got insight from this. Have a nice day
Answer: Differential Expression with limma: Contrast and Design Matrix, combinatorial ap by dariober 14k
> Is this a statistically valid approach to compare the impact of any bacterial exposure and genotype? At a glance, it seems fine to me…
Comment: Filtering Multi-sample VCF file for all except one Genotype by Pierre Lindenbaum 161k
> Don't forget to follow up on your threads. If an answer was helpful, you should upvote it; if the answer resolved your question, you shou…
Answer: Filtering VCF files based on VAF giving incorrect results by Pierre Lindenbaum 161k
using vcfilterjdk: https://jvarkit.readthedocs.io/en/latest/VcfFilterJdk/ java -jar ${JVARKIT_DIST}/jvarkit.jar vcffilterjdk …
Comment: Applying the metacell2 algorithm using python by JACKY ▴ 140
I have one more question please. When reading the h5ad file at the very beginning, do I need to perform the usual scanpy normalization step…
Comment: Using Cutadapt to trim adapters from paired-end small RNA sequence data by melissa.joubert • 0
Thank you! This was going to be my next option - to simply use the Read_1 libraries for all samples. Can I ask about the second option you…
Comment: Filtering Multi-sample VCF file for all except one Genotype by schmince • 0
Thanks, that was exactly what i needed
Comment: Benchmarking RNASeq Variant Calling Pipeline (Short Reads) by Esraa • 0
Thank you! I will try searching for this more and see if it would fit my analysis purposes.
Comment: Benchmarking RNASeq Variant Calling Pipeline (Short Reads) by Esraa • 0
Thank you so much for answering! I actually found some studies doing it the way you mentioned. I ran the GATK best practices pipeline on t…
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