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384 results • Page 3 of 8
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30
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6
replies
22k
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Tutorial: Transforming And Manipulating Color Space Reads
conversion solid
updated 14 months ago by 41k • written 11.6 years ago by 99k
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
20
votes
6
replies
5.3k
views
Tutorial: Open Targets and programmatic access
open-targets disease API drug
updated 8 months ago by 41k • written 7.2 years ago by ★ 5.2k
104
votes
6
replies
25k
views
6 follow
Tutorial: Creating workflows with snakemake and conda
workflow snakemake conda
updated 8 months ago by 41k • written 5.3 years ago by 16k
43
votes
6
replies
12k
views
Tutorial: Annotating TCGA MAFs with the latest Ensembl/Gencode transcripts
ensembl maf tcga vcf
updated 9 months ago by 41k • written 9.9 years ago by 6.0k
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 17 months ago by 41k • written 7.8 years ago by ★ 4.2k
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
36
votes
5
replies
5.9k
views
Tutorial: [Beginner] Introduction to bioinformatics file types
fastq fasta bed SAM
updated 3 months ago by ▴ 20 • written 8.4 years ago by ▴ 410
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
16
votes
5
replies
8.8k
views
Tutorial: Using The Biomart Perl Api For Simple Queries
api perl biomart
updated 9 months ago by 41k • written 11.2 years ago by 20k
70
votes
5
replies
11k
views
8 follow
Tutorial: Bioinformatics For Metagenomic Analyses
QC taxonomy metagenomics
updated 20 months ago by 41k • written 9.7 years ago by ★ 1.8k
21
votes
5
replies
6.6k
views
Tutorial: Analysis of single-cell RNA-seq data
single-cell RNA-Seq
updated 8 months ago by 41k • written 7.4 years ago by ★ 1.5k
15
votes
5
replies
15k
views
Tutorial: How to create a mutation lolliplot with GenVisR
bioconductor graphics R genvisr
updated 8 months ago by 41k • written 7.5 years ago by 20k
12
votes
5
replies
8.1k
views
Tutorial: How To Install BioPerl Without Root Privileges in Ubuntu/Linxu
bioperl
updated 8 months ago by 41k • written 7.5 years ago by ★ 9.3k
29
votes
5
replies
6.2k
views
Tutorial: Gnu Parallel Tutorial
parallel gnu-parallel
updated 9 months ago by 41k • written 10.2 years ago by ★ 4.4k
10
votes
5
replies
21k
views
Tutorial: Y-DNA and mtDNA Haplogroup Predictor
haplogroup
updated 8 months ago by 41k • written 5.4 years ago by ★ 9.3k
15
votes
5
replies
12k
views
6 follow
Tutorial: Easy way to do GO enrichment in R
enrichr RNA-Seq gene R
updated 9 months ago by 41k • written 6.0 years ago by ▴ 770
64
votes
5
replies
7.1k
views
10 follow
Tutorial: Informatics of RNA-Seq.
next-gen RNA-Seq
updated 13 months ago by 41k • written 8.3 years ago by 12k
2
votes
5
replies
2.1k
views
Tutorial: Building OMA database on SGE
oma
updated 8 months ago by 41k • written 7.5 years ago by ▴ 10
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
12
votes
5
replies
2.2k
views
Tutorial: FASTA file split
fasta
updated 8 months ago by 41k • written 3.5 years ago by 8.4k
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
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
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
24
votes
4
replies
7.2k
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
20
votes
4
replies
2.5k
views
Tutorial: Bash One-liners collection on Github
bash linux shell
updated 8 months ago by 41k • written 4.6 years ago by ▴ 180
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
28
votes
4
replies
4.2k
views
Tutorial: Modern Statistics for Modern Biology
statistics
updated 8 months ago by 41k • written 4.9 years ago by 26k
0
votes
4
replies
464
views
Tutorial: Reverse pharmacology: how to predict drugs with genes or disease names?
drugs drug-targets genes
27 days ago by Coremine Medical ▴ 20
10
votes
4
replies
11k
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 5.8k
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
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
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
20
votes
4
replies
8.4k
views
Tutorial: DE analysis by edgeR
RNA-Seq R edgeR
updated 8 months ago by 41k • written 7.2 years ago by ★ 4.2k
12
votes
4
replies
5.1k
views
Tutorial: *FREE course* Bioinformatics for Biologists: An Introduction to Linux, Bash Scripting, and R
linux R
updated 10 months ago by 41k • written 2.8 years ago by ▴ 130
1
vote
4
replies
3.2k
views
Tutorial: How to install C++ compilers/make from GNU for Gromacs?
Gromacs Cpp-compilers GNU
updated 8 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 10.8 years ago by 99k
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 3.4 years ago by ▴ 340
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
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
7
votes
3
replies
2.0k
views
Tutorial: Automated dbSNP lookup by rsID position, plus genome build liftover
rsid hg19 liftover hg38 dbsnp
updated 8 months ago by ▴ 110 • written 16 months ago by 86k
4
votes
3
replies
4.4k
views
Tutorial: How to get full taxonomy classification using taxize and myTAI
taxonomy R
updated 8 months ago by 41k • written 5.7 years ago by ★ 3.9k
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
19
votes
3
replies
13k
views
Tutorial: bedGraphToBigWig Tutorial and Report
bedGraphToBigWig
updated 17 months ago by 41k • written 7.8 years ago by ★ 9.3k
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
13
votes
3
replies
5.0k
views
Tutorial: Video: Visualization of whole genome DNA methylation data in IGB
Bismark BS-Seq RNA-Seq IGB
updated 18 months ago by 41k • written 8.7 years ago by ▴ 860
1
vote
3
replies
3.1k
views
Tutorial: resolving error of sspace_standard
software-error Assembly
updated 8 months ago by 41k • written 7.3 years ago by ▴ 300
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
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
15
votes
3
replies
4.5k
views
Tutorial: NCBI blast tutorial
ncbi blast
updated 8 months ago by 41k • written 7.6 years ago by 11k
384 results • Page 3 of 8
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C: Recommended cutoff for FDR - 0.05 or 0.1
A: Recommended cutoff for FDR - 0.05 or 0.1
A: Help with WGCNA pickSoftThreshold error
Comment: Where is the index command?
A: How To Map A Snp To A Gene Around +/- 60Kb ?
A: Gene set enrichment analysis with logFC and PValue
A: Fold change cut off enrichment analysis
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Scholar to fracarb8 ★ 1.3k
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Comment: Aligning sequences with multiple genetic codes! by pippo1980 • 0
What is Codon Alignment? When aligning DNA sequences, most algorithms only consider the best alignment for the nucleotide residues. The pr…
Comment: recommend gene ranking methods when doing GSEA by rpolicastro 12k
I tend to use shrunken log fold changes from e.g. DESeq2 to reduce the prevalence of genes with high log fold differences but very low expr…
Comment: Opinion on miRNA pipeline by Barry Digby ★ 1.3k
Feel free to take bits from this pipeline - [mirna_alignment.sh][1]. It mimicks all of the steps in nf-core/smrnaseq and the advice given b…
Comment: Genetic data QC prior to imputation by kl ▴ 10
Hi Raony, Thank you for your response. I am doing the sex check part of the QC but I only have 19 variants with MAF>0.05 and the sex check…
Comment: Multi-factor designs in DiffBind by Ram 41k
Please do not add answers unless you're answering the top level question. Instead, use `Add Comment` or `Add Reply` as appropriate. I've mo…
Comment: Where is the index command? by jkbonfield ★ 1.2k
That's a tarball of the C source code you've just unpacked. There's an "INSTALL" file with detailed instructions of how to compile the sof…
Comment: Multi-factor designs in DiffBind by g.persic1991 • 0
Hi Rory, Thanks a lot for your comment. Up to now I have performed the contrast in an explicitly way (as you suggest) using this comma…
Answer: How to avoid missannotated GO terms? by Istvan Albert 99k
The problem most likely is with the blast alignment. BLAST is a local aligner, getting a hit to another sequence does not mean that the…
Comment: Read count vs Depth by Ram 41k
Do not use spreadsheet software to view plain text files. Use a plain text utility such as BBEdit/TextWrangler/NotePad++/gedit or simple co…
Comment: vcftools by Ram 41k
What output files were you expecting? Was nothing printed on the screen at all?
Comment: Consensus peaksets in DiffBind - conceptual questinos by Rory Stark ★ 2.0k
The question of defaults for the software is often a tricky one. I do think the mutliple-replicate method is a good idea in many cases, w…
Answer: How to query 1000 genomes project VCF files for specific regions without downloa by Pierre Lindenbaum 158k
bcftools works with remote indexed VCF bcftools view "http://ftp.1000genomes.ebi.ac.uk/vol1/ftp/data_collections/1000G_2504_high_cov…
Comment: Consensus peaksets in DiffBind - conceptual questinos by Sam ▴ 300
My question was not how to do it - but conceptually, should not this be the default way to do an analysis, unless there is a good reason *n…
Comment: select unique samples in R by bk11 ★ 1.8k
Instead of `setdiff(list1$Sample_ID, list2$Sample_ID)` do this- `setdiff(list1, list2)`
Answer: Consensus peaksets in DiffBind - conceptual questinos by Rory Stark ★ 2.0k
What you describe - deriving a consensus set comprising the union of peaks called in at least two replicates of any sample group - is exact…
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