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384 results • Page 4 of 8
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12
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0
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2.5k
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Tutorial: Long versus wide data for plotting genomics data in R.
ggplot2 tidyverse data.table R
updated 8 months ago by 41k • written 3.3 years ago by 12k
11
votes
1
reply
2.5k
views
Tutorial: Guidelines for the computational analysis of single-cell RNA sequencing data
scRNA-seq
updated 8 months ago by 41k • written 2.9 years ago by ★ 25k
11
votes
7
replies
1.9k
views
Tutorial: Sequence Alignment from Scratch with BWA
alignment bwa DNA
8 months ago by barslmn ★ 2.0k
11
votes
7
replies
9.9k
views
Tutorial: ClusterProfiler A software for functional enrichment of differentially expressed genes- A tutorial
clusterProfiler Software rna-seq
updated 6 months ago by 41k • written 2.8 years ago by ▴ 360
11
votes
0
replies
6.1k
views
Tutorial: Yes .. BBMap can do that! - Part II randomreads (read simulation), demuxbyname/filterbyname, bbsplit (read binning/decontamination) and pileup (cover…
bbmap
updated 8 months ago by 41k • written 2.9 years ago by 136k
11
votes
3
replies
1.3k
views
Tutorial: Creating great documentation for bioinformatics software
Software-Documentation
updated 8 months ago by 41k • written 7.4 years ago by 7.1k
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
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
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
10
votes
2
replies
3.3k
views
Tutorial: How to find PubMed records where you were author (member) as part of a consortium
pubmed
updated 16 months ago by 41k • written 8.1 years ago by 20k
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
10
votes
2
replies
3.6k
views
Tutorial: Graph visualization with igraph in R
Visualization igraph Graph R Network
updated 7 months ago by 41k • written 6.7 years ago by 26k
10
votes
1
reply
2.2k
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 8 months ago by 41k • written 3.7 years ago by ★ 2.5k
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
10
votes
0
replies
4.2k
views
Tutorial: Yes .. BBMap can do that! - Part I : bbmap (aligner), bbduk (scan/trim), repair (fix PE reads) and reformat (format conversions)
bbmap
updated 8 months ago by 41k • written 2.9 years ago by 136k
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
10
votes
31
replies
10.0k
views
10 follow
Tutorial: OrthoMCL installation on Ubuntu Linux
ubuntu orthomcl mysql linux
updated 6 weeks ago by • 0 • written 5.9 years ago by ▴ 320
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
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
9
votes
4
replies
4.5k
views
Tutorial: Unsupervised clustering on gene expression data
gene-expression clustering RNA-seq
4 months ago by Hamid Ghaedi 3.1k
9
votes
2
replies
5.3k
views
Tutorial: From Data import to Normalization in Microarray Analysis using in R (Part I)
gene R
updated 8 months ago by 41k • written 7.5 years ago by ▴ 140
9
votes
0
replies
4.3k
views
Tutorial: Analysis of dbGaP data on the cloud
AWS dbGaP Cloud
updated 16 months ago by 41k • written 7.8 years ago by 19k
9
votes
0
replies
3.6k
views
Tutorial: Video: Intro to All New Features in IGB 8.2
R paired-end IGB
updated 21 months ago by 41k • written 9.0 years ago by ▴ 860
9
votes
0
replies
8.5k
views
Tutorial: Installing And Running Ncbi Blast
blast
updated 9 months ago by 41k • written 11.7 years ago by ▴ 540
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
9
votes
0
replies
2.5k
views
Tutorial: Introduction to Next Generation Sequencing (Part 1)
polony emulsion-pcr next-gen-sequencing
updated 13 months ago by 41k • written 8.4 years ago by ▴ 90
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
8
votes
7
replies
8.1k
views
Tutorial: Getting Cegma/Genewise To Work On Centos, Rhel
centos genewise rhel cegma
updated 22 months ago by 41k • written 10.0 years ago by ★ 2.6k
8
votes
12
replies
6.5k
views
Tutorial: Create your own VPN to access work resources from home
tinyproxy OpenVPN VPN
updated 8 months ago by 41k • written 7.5 years ago by 13k
8
votes
19
replies
13k
views
9 follow
Tutorial: A:orthomcl with local mysql server on linux server, complete install
mysql orthomcl
updated 9 months ago by 41k • written 9.0 years ago by ▴ 600
8
votes
3
replies
2.6k
views
Tutorial: Free online interactive Ensembl training
ensembl training genome
updated 17 months ago by 41k • written 7.8 years ago by 23k
8
votes
1
reply
1.3k
views
Tutorial: Split a 'linearised' (flattened) FASTA sequence into multi-line using AWK
fasta awk
updated 8 months ago by 41k • written 2.7 years ago by 86k
8
votes
9
replies
11k
views
Tutorial: Extracting subset of records from FASTA/FASTQ files based on exact/pattern matches of IDs (ONE-LINERS)
fastq fasta
updated 9 months ago by 41k • written 9.6 years ago by ★ 1.8k
8
votes
0
replies
2.5k
views
Tutorial: Pipes in R: An introduction and some advanced tips and tricks.
R
2.7 years ago by rpolicastro 12k
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
8
votes
17
replies
2.9k
views
Tutorial: Simple approach to RNA-seq (T-Bioinfo platform)
alignment next-gen-sequencing RNA-seq
updated 15 months ago by 41k • written 8.2 years ago by ▴ 340
7
votes
2
replies
1.6k
views
Tutorial: A tale of two heatmap function
clustering heatmap
updated 8 months ago by 41k • written 7.2 years ago by ★ 3.6k
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
7
votes
14
replies
3.2k
views
6 follow
Tutorial: Install required dependencies for GATK4 on remote server without root privilege
gatk
updated 13 months ago by • 0 • written 21 months ago by ▴ 30
7
votes
1
reply
1.9k
views
Tutorial: A Guide to DNA Sequencing Techniques Part 1
dna sanger sequencing pyrosequencing
updated 8 months ago by 41k • written 8.4 years ago by ▴ 410
7
votes
0
replies
5.2k
views
Tutorial: Mothur Analyzing 16S Of Ngs High Through-Put Sequencing
next-gen
updated 9 months ago by 41k • written 11.5 years ago by ▴ 120
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
7
votes
0
replies
3.0k
views
Tutorial: On the concept of constant or intercept used in Differential Expression (DE) analysis
regression limma DESeq2
updated 8 months ago by 41k • written 7.6 years ago by ★ 5.1k
7
votes
8
replies
3.3k
views
Tutorial: Determine if a transcription factor is bound with CENTIPEDE
ChIP-Seq transcription-factor DNase-Seq CENTIPEDE
updated 12 months ago by 41k • written 8.4 years ago by ★ 2.2k
7
votes
0
replies
4.6k
views
Tutorial: How To Perform A Hierarchical Clustering Using Interactive Heatmaps From Gitools?
clustering
updated 9 months ago by 41k • written 9.7 years ago by ▴ 990
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
7
votes
2
replies
3.5k
views
Tutorial: List Of Tools For Mapping High-Throughput Sequencing Data (2012)
next-gen mapping
updated 9 months ago by 41k • written 11.2 years ago by 11k
7
votes
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
6
votes
0
replies
3.3k
views
Tutorial: How to download GEO data Quickly and easily
geo RNA-Seq R data-mining
9 months ago by Novogene ▴ 360
6
votes
3
replies
4.4k
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
384 results • Page 4 of 8
Recent Votes
Answer: batch effect in RNA-Seq
Answer: Are we tricking ourselves with batch effect correction?
A: How to do DMR analysis with BiSeq (for RRBS methylation data)?
A: How to do DMR analysis with BiSeq (for RRBS methylation data)?
Answer: 1000 genomes data?
Answer: General question about clustering in scRNAseq
Answer: General question about clustering in scRNAseq
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Recent Replies
Comment: How to avoid missannotated GO terms? by Dr.Animo ▴ 80
These kind of missannotations are assigned to multiple plant proteins except few like Arabidopsis thaliana and Zea maize. The problem is if…
Answer: SQL request from NCBI metadata and stat_analysis tables by zorbax ▴ 600
I think what you are looking for is the LEFT JOIN approach, where you can select a specific phylum. Have you tried this (next you should or…
Comment: Convert NCBI Downloaded files to ANNOVAR format by Ram 41k
You may also find tools such as vcfanno and bcftools easier to work with, if you don't want to spend too much time reformatting dictionary …
Comment: Convert NCBI Downloaded files to ANNOVAR format by robert • 0
Ok I guess I got confused because there is support for, for example gff3-solid, but not directly gff files. I will have a look at VEP, but …
Comment: How to perform quality control for sex when there are no variants after threshol by kl ▴ 10
I am trying with PLINK --check sex. Would an option be to merge my data with 1000 genomes European allele frequencies and redo the threshol…
Comment: Convert NCBI Downloaded files to ANNOVAR format by Ram 41k
The documentation is clear on this: `convert2annovar.pl` is used to convert input (genotype) files to ANNOVAR format. It is not used on dic…
Comment: How to perform quality control for sex when there are no variants after threshol by Ram 41k
The simple answer is you can't. Also, is there a reason why your title and your post body have the same content? Use a concise title and el…
Comment: Differential expression using Bowtie2 by ATpoint 78k
You cannot just randomly pull data from NCBI and then quantitatively compare them. RNA-seq is inherently a relative measure and quantitativ…
Comment: how to remove multiple columns from a file in R by Ram 41k
Accept their answer and then add your own and accept that as well.
Comment: how to remove multiple columns from a file in R by Ram 41k
Please stop asking basic R/programming questions and use Google to learn the underlying concepts. A simple search is the way to start: http…
Answer: get gene name from rsID by Ram 41k
Not all variants fall in coding regions. `rs2873296` for example is `NC_000001.10:g.21721038A>G`, which is in a non-coding region.
Comment: Differential expression using Bowtie2 by 8d8fc19e • 0
NCBI's Sequence Read Archive gives me the transcriptome of an organ (the RNA-seq data) which can be downloaded either as a .fasta or .fastq…
Comment: Differential expression using Bowtie2 by ATpoint 78k
Which will be obtained from NCBI...what does that mean, and which data do you have?
Comment: fgsea leading edge genes by ATpoint 78k
Just check the rank of these genes in the ranked data that were input to fgsea, then you know.
Answer: fgsea leading edge genes by Yuri ★ 1.6k
I asked the same question myself. I looked at the code of `calcGseaStat` function in `fgsea` package, and it appears that leading edge gene…
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