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318 results • Page 3 of 7
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Tutorial: How to create a mutation lolliplot with GenVisR
bioconductor graphics R genvisr
updated 7 months ago by 41k • written 7.5 years ago by 20k
1
vote
4
replies
3.2k
views
Tutorial: Applying machine learning to NGS transcriptomic data
next-gen RNA-Seq
updated 6 months ago by 41k • written 5.6 years ago by ▴ 340
10
votes
4
replies
10k
views
Tutorial: Using the MinION MinKNOW software on Ubuntu 1604
long-reads oxford-nanopore minion
updated 8 months ago by 41k • written 4.4 years ago by 5.7k
20
votes
4
replies
14k
views
Tutorial: How To Install A Specific Cdf Package For Use In Bioconductor
bioconductor affymetrix
updated 9 months ago by 41k • written 10.7 years ago by 20k
20
votes
4
replies
2.5k
views
Tutorial: Bash One-liners collection on Github
bash linux shell
updated 8 months ago by 41k • written 4.5 years ago by ▴ 180
3
votes
4
replies
4.3k
views
Tutorial: gencore: a tool to reduce sequencing noises by generating consensus reads
consensus OpenGene sequencing-noise
updated 6 months ago by 41k • written 5.6 years ago by ★ 2.5k
0
votes
4
replies
437
views
Tutorial: Reverse pharmacology: how to predict drugs with genes or disease names?
drugs drug-targets genes
18 days ago by Coremine Medical ▴ 20
3
votes
4
replies
3.5k
views
Tutorial: Gene Set Enrichment Analysis on T-BioInfo
gene RNA-Seq
updated 6 months ago by 41k • written 5.1 years ago by ▴ 340
12
votes
4
replies
5.1k
views
Tutorial: *FREE course* Bioinformatics for Biologists: An Introduction to Linux, Bash Scripting, and R
linux R
updated 9 months ago by 41k • written 2.8 years ago by ▴ 130
28
votes
4
replies
4.1k
views
Tutorial: Modern Statistics for Modern Biology
statistics
updated 8 months ago by 41k • written 4.8 years ago by 26k
10
votes
4
replies
3.4k
views
Tutorial: CorLevelPlot - Visualise correlation results, e.g., clinical parameter correlations
correlation corlevelplot
updated 6 months ago by 41k • written 5.8 years ago by 86k
15
votes
4
replies
4.4k
views
Tutorial: RNASeq tutorial for gene differential expression analysis
Transcriptomics bioconductor RNA-Seq R
updated 8 months ago by 41k • written 3.3 years ago by ▴ 340
9
votes
4
replies
4.5k
views
Tutorial: Unsupervised clustering on gene expression data
gene-expression clustering RNA-seq
3 months ago by Hamid Ghaedi 3.1k
1
vote
4
replies
3.2k
views
Tutorial: How to install C++ compilers/make from GNU for Gromacs?
Gromacs Cpp-compilers GNU
updated 7 months ago by 41k • written 7.5 years ago by ▴ 10
19
votes
4
replies
8.7k
views
Tutorial: Rna Seq Experimental Design For Measuring Differential Gene Expression
RNA-seq
updated 9 months ago by 41k • written 10.7 years ago by 99k
24
votes
4
replies
7.1k
views
Tutorial: Using EnrichedHeatmap for visualization of NGS experiments
heatmap chip-seq atac-seq EnrichedHeatmap
updated 8 months ago by 41k • written 4.3 years ago by 78k
6
votes
4
replies
7.3k
views
Tutorial: Overlay Multiple Tracks In Ucsc Browser [Quick Minimal Tutorial]
visualization ChIP-seq RNA-seq ucsc-genome-browser bigwig
updated 9 months ago by 41k • written 10.7 years ago by 11k
32
votes
4
replies
7.3k
views
Tutorial: Fast LD computation from VCF files using tomahawk
ld snp vcf vcftools bcftools
updated 8 months ago by 41k • written 5.1 years ago by ★ 1.6k
20
votes
4
replies
8.4k
views
Tutorial: DE analysis by edgeR
RNA-Seq R edgeR
updated 7 months ago by 41k • written 7.2 years ago by ★ 4.2k
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
3
replies
1.3k
views
Tutorial: Creating great documentation for bioinformatics software
Software-Documentation
updated 7 months ago by 41k • written 7.4 years ago by 7.1k
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 6.6 years ago by ★ 1.2k
3
votes
3
replies
2.4k
views
Tutorial: Generating count matrix for STAR counts in GDC v32.0 for RNA-Seq
GDC TCGABiolinks STAR
updated 9 months ago by 41k • written 19 months ago by ★ 3.3k
5
votes
3
replies
5.1k
views
Tutorial: bam2rpkm by bedtools
bam RNA-Seq bedtools rpkm
updated 8 months ago by • 0 • written 6.1 years ago by ▴ 130
1
vote
3
replies
3.1k
views
Tutorial: resolving error of sspace_standard
software-error Assembly
updated 7 months ago by 41k • written 7.3 years ago by ▴ 300
13
votes
3
replies
14k
views
Tutorial: Plotting the coverage and depth (Y-axis) statistics of a bam file along the genome (X-axis), using Samtools, awk and R.
genome plot coverage samtools
updated 3 months ago by ▴ 20 • written 6.7 years ago by ★ 1.6k
50
votes
3
replies
4.5k
views
Tutorial: [[ Please read before posting a question ::: How To Ask A Good Question ]]
how-to
updated 8 months ago by 41k • written 4.9 years ago by 78k
7
votes
3
replies
2.0k
views
Tutorial: Automated dbSNP lookup by rsID position, plus genome build liftover
rsid hg19 liftover hg38 dbsnp
updated 7 months ago by ▴ 110 • written 15 months ago by 86k
10
votes
3
replies
4.3k
views
Tutorial: Video: Alternative Splicing and Primer Design
RNA-Seq IGB
updated 10 months ago by 41k • written 9.2 years ago by ▴ 860
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 5.9 years ago by ▴ 100
51
votes
3
replies
22k
views
Tutorial: Sam File Format - Lesser Known Tips And Tricks
sam
updated 9 months ago by 41k • written 10.9 years ago by ▴ 300
15
votes
3
replies
4.5k
views
Tutorial: NCBI blast tutorial
ncbi blast
updated 7 months ago by 41k • written 7.6 years ago by 11k
6
votes
3
replies
5.6k
views
Tutorial: High Throughput Sequence Analysis With R And Bioconductor
bioconductor
updated 9 months ago by 41k • written 11.4 years ago by 99k
4
votes
3
replies
4.3k
views
Tutorial: How to get full taxonomy classification using taxize and myTAI
taxonomy R
updated 8 months ago by 41k • written 5.6 years ago by ★ 3.9k
44
votes
3
replies
12k
views
Tutorial: A Wet-Lab Guide to 'what I wish I had known' for Computational Biology
bioinformatics computational-biology
updated 7 months ago by 41k • written 7.7 years ago by ★ 3.2k
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 6.7 years ago by ▴ 20
0
votes
3
replies
50k
views
Tutorial: Installation VMD on LINUX_64
gromacs VMD
updated 7 months ago by 41k • written 7.5 years ago by ▴ 10
9
votes
3
replies
4.1k
views
Tutorial: Ht Sequence Analysis With R And Bioconductor By The Bioinformatics Center At Uc Riverside
bioconductor
updated 9 months ago by 41k • written 11.3 years ago by 99k
5
votes
3
replies
4.1k
views
Tutorial: Chip Seq Review Papers
chip-seq
updated 9 months ago by 41k • written 11.0 years ago by ▴ 80
6
votes
3
replies
4.3k
views
Tutorial: Principles and Workflow of 16S/18S/ITS Amplicon Sequencing
alignment sequencing RNA-seq gene
updated 8 months ago by 41k • written 5.1 years ago by ▴ 40
1
vote
3
replies
782
views
Tutorial: Gibbs Sampling Algorithm Implementation for Searching DNA Motifs
montecarlo DNA motif gibbssampling splice
8 months ago by barslmn ★ 2.0k
4
votes
2
replies
1.9k
views
Tutorial: Prediction of Ribosomal RNA Genes Using RNAmmer Software
Annotation rRNA RNAmmer Genome
4 months ago by Dr.Animo ▴ 80
3
votes
2
replies
2.5k
views
Tutorial: Continuing Education (Pipelines): Best blogs, Online Lectures, Workshops, etc..
conferences Workshops
updated 6 months ago by 41k • written 6.6 years ago by ▴ 100
2
votes
2
replies
1.9k
views
Tutorial: Human mitochondrial DNA annotation in SnpEff
chrMT SNP snpEff
updated 8 months ago by 41k • written 3.4 years ago by 3.2k
1
vote
2
replies
1.3k
views
Tutorial: ViennaRNA package installation in Windows
windows rna mfold viennarna
updated 5 months ago by 41k • written 14 months ago by ▴ 20
4
votes
2
replies
7.1k
views
Tutorial: Analyzing Genomewide Association Study Data: A Tutorial Using Plink
plink gwas
updated 9 months ago by 41k • written 11.5 years ago by 99k
6
votes
2
replies
2.6k
views
Tutorial: Tutorial Bioinformatics Static Website
website
updated 9 months ago by 41k • written 9.8 years ago by ▴ 610
9
votes
2
replies
5.3k
views
Tutorial: From Data import to Normalization in Microarray Analysis using in R (Part I)
gene R
updated 7 months ago by 41k • written 7.5 years ago by ▴ 140
4
votes
2
replies
3.5k
views
Tutorial: Introduce OpenGene: an open source library for processing NGS data
NGS sequencing Julia OpenGene
updated 8 months ago by 41k • written 7.8 years ago by ★ 2.5k
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 6.6 years ago by 26k
318 results • Page 3 of 7
Recent Votes
Answer: How should I run ssgsea analysis ?
Comment: Parsing XML file from dbGaP
Comment: Discrepancy in total number of bases in trimmed read1 and read2 files after BBDu
Comment: SPAdes error: finished abnormally, OS return value: 21
Comment: Plotting a pvalue threshold for an FDR corrected pvalue <.05 when thats not pres
Comment: unicycler error : [Errno 13] Permission denied:
Comment: unicycler error : [Errno 13] Permission denied:
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Comment: AttributeError: module 'collections' has no attribute 'Hashable' by jiyoung ▴ 20
Currently I am experiencing the same problem. Have you solved this?
Comment: Help doing differential expression analysis -experimental design and gProfiler T by rajabolacuan • 0
Good Information Sir
Answer: Viral genes not showing up in combined mouse+virus alignment by cook.675 ▴ 200
Hello I was curious to follow up and wonder if anyone knew why the viral genes are not showing up in the count matrix? I can't seem to solv…
Comment: Discrepancy in total number of bases in trimmed read1 and read2 files after BBDu by CTLong ▴ 10
That makes sense. Thanks for the reminder.
Comment: bwa mem hangs after a few thousand reads by GenoMax 136k
Then you probably are best served by talking with your local sys admins to see where the issue may be.
Comment: Discrepancy in total number of bases in trimmed read1 and read2 files after BBDu by GenoMax 136k
> even if tpe and tbo are trailing after adapter and quality trimming Priority/order of operations in coded in the program. Brian will be …
Comment: bwa mem hangs after a few thousand reads by cee28 • 0
Actually, I originally did both of those things that you suggested. My original command at the top of the post was submitted to our cluster…
Comment: Discrepancy in total number of bases in trimmed read1 and read2 files after BBDu by CTLong ▴ 10
The number of bases is still different even if `tpe` and `tbo` are trailing after adapter and quality trimming. So far for the RNA-seq proj…
Comment: Discrepancy in total number of bases in trimmed read1 and read2 files after BBDu by GenoMax 136k
No there should not be much impact unless one of the reads has become substantially short compared to its mate. Strictly speaking you don't…
Comment: bwa mem hangs after a few thousand reads by GenoMax 136k
> I am running this on a HPC cluster. This is a guess but if you are actually running this on a cluster then it is possible that you need …
Comment: Discrepancy in total number of bases in trimmed read1 and read2 files after BBDu by CTLong ▴ 10
Thanks GenoMax for the reply. That being said, does this difference in total bases between read1 and read2 have an effect in subsequent rea…
Comment: CHIPSEQ : Cut AND Run , DiffBind Parameters by DINESHR • 0
Here are my PCA results plotted through Diffbind and Correlation heat map by deeptools shows some clustering in the samples @atpoint ![e…
Comment: Plotting a pvalue threshold for an FDR corrected pvalue <.05 when thats not pres by dsull ★ 5.0k
Yeah, sometimes it looks "prettier" to plot p-value rather than adjusted p-value; although either one is technically ok to plot (even multi…
Comment: How to get unaligned reads and aligned reads into separate files from SAM/BAM? by rpolicastro 12k
I suppose if you really wanted to do it in one pass pysam would be an option. Courtesy of ChatGPT with a few modifications, and tested to s…
Comment: frequency plot for peaks by Ankit ▴ 400
what is your txdb? can you explain your experiment in detail?
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