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123 results • Page 2 of 3
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32
votes
4
replies
6.4k
views
Tutorial: Fast LD computation from VCF files using tomahawk
ld snp vcf vcftools bcftools
updated 8 days ago by 38k • written 4.4 years ago by ★ 1.5k
23
votes
4
replies
6.2k
views
Tutorial: Using EnrichedHeatmap for visualization of NGS experiments
heatmap chip-seq atac-seq EnrichedHeatmap
updated 11 days ago by 38k • written 3.6 years ago by 70k
19
votes
9
replies
6.0k
views
8 follow
Tutorial: Interactive Perl Learning
perl
updated 26 days ago by 38k • written 9.8 years ago by 9.5k
29
votes
5
replies
5.9k
views
Tutorial: Gnu Parallel Tutorial
parallel gnu-parallel
updated 25 days ago by 38k • written 9.5 years ago by ★ 4.3k
20
votes
7
replies
5.6k
views
Tutorial: Showing up and down regulated GO and pathway using enrichR and ggplot2
ggplot2 RNA-Seq R
updated 10 days ago by 38k • written 4.4 years ago by ▴ 740
14
votes
7
replies
5.4k
views
Tutorial: Visualization of ChIP-Seq peak overlaps using HOMER mergePeaks and UpSetR
ChIP-Seq peaks R HOMER
updated 10 days ago by 38k • written 6.9 years ago by ★ 3.3k
34
votes
15
replies
5.0k
views
6 follow
Tutorial: How to do data cleaning for VCF genetic file
vcf
updated 10 days ago by 38k • written 3.8 years ago by ★ 9.3k
3
votes
2
replies
4.9k
views
Tutorial: Reorder Vcf Files
vcf
updated 29 days ago by 38k • written 9.9 years ago by ▴ 60
20
votes
6
replies
4.8k
views
Tutorial: Open Targets and programmatic access
open-targets disease API drug
updated 10 days ago by 38k • written 6.5 years ago by ★ 5.2k
12
votes
1
reply
4.8k
views
Tutorial: scRNA-seq CITE-seq-count bioinformatics
CITE-seq-count scRNA-seq RNA-Seq
updated 10 days ago by 38k • written 3.0 years ago by 4.6k
12
votes
31
replies
4.7k
views
6 follow
Tutorial: gene set filter/selection for training ab initio annotation tools
geneset genome gene abinitio
updated 16 days ago by 38k • written 3.6 years ago by 7.7k
20
votes
10
replies
4.6k
views
Tutorial: Finding the significance of the overlap between 2 or more gene sets using simulation in R.
tidyverse gene R
updated 11 days ago by 38k • written 2.6 years ago by 11k
7
votes
0
replies
4.5k
views
Tutorial: How To Perform A Hierarchical Clustering Using Interactive Heatmaps From Gitools?
clustering
updated 21 days ago by 38k • written 9.0 years ago by ▴ 990
5
votes
3
replies
4.5k
views
Tutorial: bam2rpkm by bedtools
bam RNA-Seq bedtools rpkm
updated 9 days ago by • 0 • written 5.4 years ago by ▴ 130
10
votes
0
replies
4.4k
views
Tutorial: Yes .. BBMap can do that! - Part II randomreads (read simulation), demuxbyname/filterbyname, bbsplit (read binning/decontamination) and pileup (cover…
bbmap
updated 11 days ago by 38k • written 2.2 years ago by 127k
10
votes
7
replies
4.4k
views
Tutorial: STARsolo config for 10x Chromium v1, v2, v3
Chromium 10x STARsolo STAR
updated 11 days ago by 38k • written 2.5 years ago by 84k
6
votes
10
replies
4.3k
views
Tutorial: Differentially methylated regions: Easy & Fast Identification and ANnoTation
DMR dna-methylation
updated 11 days ago by 38k • written 5.1 years ago by ▴ 340
6
votes
3
replies
4.1k
views
Tutorial: Principles and Workflow of 16S/18S/ITS Amplicon Sequencing
alignment sequencing RNA-seq gene
updated 10 days ago by 38k • written 4.4 years ago by ▴ 40
15
votes
4
replies
4.1k
views
Tutorial: RNASeq tutorial for gene differential expression analysis
Transcriptomics bioconductor RNA-Seq R
updated 11 days ago by 38k • written 2.7 years ago by ▴ 300
50
votes
3
replies
4.0k
views
Tutorial: [[ Please read before posting a question ::: How To Ask A Good Question ]]
how-to
updated 10 days ago by 38k • written 4.2 years ago by 70k
4
votes
3
replies
3.9k
views
Tutorial: How to get full taxonomy classification using taxize and myTAI
taxonomy R
updated 10 days ago by 38k • written 5.0 years ago by ★ 3.9k
2
votes
0
replies
3.8k
views
Tutorial: Calculation of TSS Scores for ATAC-seq Data
next-gen-sequencing
updated 10 days ago by 38k • written 3.7 years ago by ▴ 20
28
votes
4
replies
3.7k
views
Tutorial: Modern Statistics for Modern Biology
statistics
updated 10 days ago by 38k • written 4.2 years ago by 26k
5
votes
0
replies
3.5k
views
Tutorial: Yes .. BBMap can do that! - Part III clumpify (mark (and dedupe) duplicates without alignment), mutate (create mutant genomes) and other miscellaneou…
bbmap
updated 11 days ago by 38k • written 2.2 years ago by 127k
3
votes
0
replies
3.4k
views
Tutorial: Video Tutorial On Conducting Whole-Exome Sequencing Research
exome-sequencing
updated 26 days ago by 38k • written 9.8 years ago by 9.5k
6
votes
0
replies
3.4k
views
Tutorial: How to predict genes using a two-pass (iterative) MAKER2 workflow
Assembly
updated 19 days ago by 38k • written 8.8 years ago by 7.7k
4
votes
2
replies
3.3k
views
Tutorial: Introduce OpenGene: an open source library for processing NGS data
NGS sequencing Julia OpenGene
updated 10 days ago by 38k • written 7.1 years ago by ★ 2.4k
6
votes
1
reply
2.8k
views
Tutorial: Practical Guidelines for the Comprehensive Analysis of ChIP-seq Data
ChIP-Seq peak-calling sequencing
updated 19 days ago by 38k • written 8.9 years ago by ▴ 220
14
votes
2
replies
2.8k
views
Tutorial: Methylation Analysis Tutorial in R_part2
cancer methylation RNA-Seq R
updated 11 days ago by 38k • written 2.5 years ago by 2.9k
3
votes
0
replies
2.8k
views
Tutorial: Sorting GFF/GTF files
gtf gff
updated 16 days ago by 38k • written 2.7 years ago by 7.7k
10
votes
0
replies
2.7k
views
Tutorial: Yes .. BBMap can do that! - Part I : bbmap (aligner), bbduk (scan/trim), repair (fix PE reads) and reformat (format conversions)
bbmap
updated 11 days ago by 38k • written 2.2 years ago by 127k
15
votes
2
replies
2.7k
views
Tutorial: Introduction to bedtools.
bedtools
updated 16 days ago by 38k • written 8.4 years ago by 11k
5
votes
0
replies
2.6k
views
Tutorial: How to run CWL with Nextflow
cwl nextflow
updated 10 days ago by 38k • written 3.1 years ago by ★ 3.3k
2
votes
1
reply
2.4k
views
Tutorial: How to extract and filter SNP data from the genotyping-by-sequencing (GBS) data in vcf format using bcftools
bcftools SNP-Filtering VCF
updated 10 days ago by 38k • written 3.1 years ago by ▴ 10
6
votes
2
replies
2.4k
views
Tutorial: Tutorial Bioinformatics Static Website
website
updated 22 days ago by 38k • written 9.1 years ago by ▴ 610
0
votes
1
reply
2.4k
views
Tutorial: Getting the lineage of an organism from NCBI taxonomy data
biosql python taxonomy
updated 11 days ago by 38k • written 4.6 years ago by ▴ 310
5
votes
1
reply
2.3k
views
Tutorial: Nice simple interactive Vim tutorial
vim linux
updated 16 days ago by 38k • written 8.4 years ago by 9.5k
20
votes
4
replies
2.2k
views
Tutorial: Bash One-liners collection on Github
bash linux shell
updated 10 days ago by 38k • written 3.9 years ago by ▴ 180
11
votes
1
reply
2.2k
views
Tutorial: Guidelines for the computational analysis of single-cell RNA sequencing data
scRNA-seq
updated 11 days ago by 38k • written 2.2 years ago by ★ 23k
26
votes
0
replies
2.1k
views
Tutorial: Resources / databases for clinical interpretation of cancer variants
interpretation cancer annotation variant
updated 11 days ago by 38k • written 3.4 years ago by 19k
12
votes
0
replies
2.0k
views
Tutorial: Long versus wide data for plotting genomics data in R.
ggplot2 tidyverse data.table R
updated 10 days ago by 38k • written 2.6 years ago by 11k
10
votes
1
reply
2.0k
views
Tutorial: introduce a tool for fast identification of SARS-CoV-2 and other microbes from sequencing data
SARS-CoV-2 fastv COVID-19
updated 11 days ago by 38k • written 3.0 years ago by ★ 2.4k
5
votes
2
replies
2.0k
views
Tutorial: NCBI submissions: SRA and TSA
NCBI TSA SRA RNA-Seq
updated 8 days ago by 38k • written 4.3 years ago by ▴ 50
5
votes
2
replies
2.0k
views
Tutorial: Using Bedtools Closest (closestBed) to make distance histograms of protein binding frequency near all types of pre-RNA junctions (e.g. exon-intron an…
preRNA closestBed bedtools-closest bedtools
updated 10 days ago by 38k • written 4.2 years ago by ▴ 10
4
votes
2
replies
2.0k
views
Tutorial: Apply beagle5.0 to make imputation and phasing under CentOS and PBS
beagle5.0 beagle
updated 11 days ago by 38k • written 3.8 years ago by ★ 9.3k
0
votes
0
replies
2.0k
views
Tutorial: Protein expression analysis
protein-analysis
updated 4 days ago by 38k • written 8.0 years ago by • 0
0
votes
0
replies
2.0k
views
Tutorial: Using OpenEye software for substructure alignments and best-matching low-energy conformer overlays
rmsd alignment openeye
updated 18 days ago by 38k • written 8.7 years ago by ▴ 140
3
votes
2
replies
1.9k
views
Tutorial: Continuing Education (Pipelines): Best blogs, Online Lectures, Workshops, etc..
blogs Workshops conferences tutorials
updated 26 days ago by ▴ 970 • written 5.9 years ago by ▴ 100
1
vote
0
replies
1.9k
views
Tutorial: A short primer to pairwise alignment
pairwise-alignment blastp pam blosum
updated 1 day ago by 38k • written 7.7 years ago by ▴ 370
12
votes
4
replies
1.8k
views
Tutorial: Tutorials for Library Normalization in DESeq2 and EdgeR
EdgeR DESeq2
updated 2 days ago by 38k • written 5.5 years ago by ▴ 570
123 results • Page 2 of 3
Recent Votes
NCBI's IgBLAST version 1.21.0 is now available
Read lengths greater than insert length
Answer: Read lengths greater than insert length
How to find promoter sequence of a gene?
Answer: How to find promoter sequence of a gene?
Comment: How to find promoter sequence of a gene?
Answer: Is it possible to do DGE analysis using log 2 normalized data with EdgeR ?
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Recent Replies
Comment: Is it possible to do DGE analysis using log 2 normalized data with EdgeR ? by seidel 11k
What technology is the GEO data set derived from? Signal intensity implies a fluorescence read out (i.e. microarray). If that's the case, y…
Comment: Log2 FC Threshold by seidel 11k
Given that 0.2 is a 1.15 fold change (2^0.2) you're right to be skeptical, but there's no clear answer as to the significance. Consider tha…
Comment: Read lengths greater than insert length by GenoMax 127k
As I said above the adapters are each ~60 bp long so they add ~120 bp (5' and 3' end adapters) to the length of the DNA fragment. What you …
Comment: Problem with fatsq-dump by GenoMax 127k
Looks like the developers have an answer for this error: https://github.com/ncbi/sra-tools/issues/139 At least the program seems to be ins…
Comment: Read lengths greater than insert length by shpak.max ▴ 30
I'm not claiming that all fragment lengths are exactly 50, the typical range for my data is 45-60. However, my read lengths are all 150, so…
Answer: Read lengths greater than insert length by GenoMax 127k
Illumina libraries are made by adding adapters to the ends of DNA fragment(s). Those adapters themselves are about 60 nucleotides long. Not…
Answer: How to get fraction of unspliced reads for specific gene from scRNAseq Cell Rang by Rob 5.9k
If you have the raw data, you can easily get this information using [alevin-fry](https://www.nature.com/articles/s41592-022-01408-3). It pr…
Answer: Matching gene-expression data with clinical data: best practices. by pilargmarch ▴ 60
I really like using [the R/Bioconductor package TCGAbiolinks][1], it gives you clinical and expression data by patient ID. [1]: http…
Comment: Problem with fatsq-dump by Utpal • 0
with the command which fastq-dump it returns: ~/.conda/envs/sratoolkit_env/bin/fastq-dump With fastq-dump I get the following error …
Comment: Calculation method of RMSMappingQuality by zhangfish ▴ 40
Maybe, I think the formal (1) is correct for most situations (for example the earlier version of GATK). However, there are some changes in …
Comment: error in downloading of some accesions with fastq-dump by Utpal • 0
Hi, could you please let me know how to upgrade sratoolkit in centos? Thanks and regards,
Answer: How to get fraction of unspliced reads for specific gene from scRNAseq Cell Rang by benformatics 3.5k
I don't think you can get that information specifically: https://kb.10xgenomics.com/hc/en-us/articles/360021902671-Can-we-detect-splice-va…
Comment: Remove part of headers in FASTA file by Pierre Lindenbaum 153k
Use `cut -d ' '`
Comment: Problem running interproscan-5.15-54.0 for protein sequences by Pratyay • 0
Hi, can you guide me how to compile the src folder? Many thanks!
Comment: Matching gene-expression data with clinical data: best practices. by krushnach80 ★ 1.1k
You can check [this][1] [1]: https://www.linkedomics.org/
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