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358 results • Page 4 of 8
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11
votes
2
replies
7.4k
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 25 days ago by 39k • written 6.2 years ago by ★ 1.5k
11
votes
7
replies
7.3k
views
Tutorial: ClusterProfiler A software for functional enrichment of differentially expressed genes- A tutorial
clusterProfiler Software rna-seq
updated 17 days ago by 39k • written 2.3 years ago by ▴ 300
11
votes
6
replies
4.6k
views
Tutorial: sharing some naive codes for microarray normalization in R with whom are too new in R alike me
R
updated 10 months ago by 39k • written 7.3 years ago by ★ 4.2k
11
votes
3
replies
1.2k
views
Tutorial: Creating great documentation for bioinformatics software
Software-Documentation
updated 8 weeks ago by 39k • written 6.9 years ago by 7.0k
11
votes
1
reply
2.3k
views
Tutorial: Guidelines for the computational analysis of single-cell RNA sequencing data
scRNA-seq
updated 11 weeks ago by 39k • written 2.4 years ago by ★ 23k
11
votes
7
replies
13k
views
Tutorial: Removing rows with duplicate values based on 1 or more key values - linux awk
awk linux bash
updated 20 days ago by 39k • written 5.7 years ago by 85k
10
votes
3
replies
4.2k
views
Tutorial: Video: Alternative Splicing and Primer Design
RNA-Seq IGB
updated 4 months ago by 39k • written 8.7 years ago by ▴ 860
10
votes
1
reply
7.7k
views
Tutorial: How to select reads with specific flag using samtools
next-gen-sequencing
updated 20 days ago by 39k • written 5.8 years ago by ▴ 110
10
votes
1
reply
2.1k
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 weeks ago by 39k • written 3.2 years ago by ★ 2.4k
10
votes
0
replies
3.1k
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 weeks ago by 39k • written 2.4 years ago by 129k
10
votes
2
replies
3.2k
views
Tutorial: How to find PubMed records where you were author (member) as part of a consortium
pubmed
updated 9 months ago by 39k • written 7.6 years ago by 20k
10
votes
5
replies
19k
views
Tutorial: Y-DNA and mtDNA Haplogroup Predictor
haplogroup
updated 11 weeks ago by 39k • written 4.9 years ago by ★ 9.3k
10
votes
7
replies
1.3k
views
Tutorial: Sequence Alignment from Scratch with BWA
alignment bwa DNA
9 weeks ago by barslmn ★ 1.6k
10
votes
4
replies
9.5k
views
Tutorial: Using the MinION MinKNOW software on Ubuntu 1604
long-reads oxford-nanopore minion
updated 11 weeks ago by 39k • written 3.9 years ago by 4.8k
10
votes
0
replies
4.9k
views
Tutorial: Yes .. BBMap can do that! - Part II randomreads (read simulation), demuxbyname/filterbyname, bbsplit (read binning/decontamination) and pileup (cover…
bbmap
updated 11 weeks ago by 39k • written 2.4 years ago by 129k
10
votes
2
replies
3.4k
views
Tutorial: Graph visualization with igraph in R
Visualization igraph Graph R Network
updated 25 days ago by 39k • written 6.2 years ago by 26k
10
votes
4
replies
2.9k
views
Tutorial: CorLevelPlot - Visualise correlation results, e.g., clinical parameter correlations
correlation corlevelplot
updated 17 days ago by 39k • written 5.3 years ago by 85k
9
votes
0
replies
2.4k
views
Tutorial: Introduction to Next Generation Sequencing (Part 1)
polony emulsion-pcr next-gen-sequencing
updated 7 months ago by 39k • written 7.9 years ago by ▴ 90
9
votes
5
replies
2.0k
views
Tutorial: What is new in samtools release 1.5 [Solstice Release] (21st June 2017)
samtools
updated 21 days ago by 39k • written 5.9 years ago by 98k
9
votes
2
replies
5.2k
views
Tutorial: From Data import to Normalization in Microarray Analysis using in R (Part I)
gene R
updated 8 weeks ago by 39k • written 7.0 years ago by ▴ 140
9
votes
0
replies
3.4k
views
Tutorial: Video: Intro to All New Features in IGB 8.2
R paired-end IGB
updated 15 months ago by 39k • written 8.5 years ago by ▴ 860
9
votes
0
replies
4.2k
views
Tutorial: Analysis of dbGaP data on the cloud
AWS dbGaP Cloud
updated 10 months ago by 39k • written 7.3 years ago by 19k
9
votes
0
replies
8.2k
views
Tutorial: Installing And Running Ncbi Blast
blast
updated 3 months ago by 39k • written 11.2 years ago by ▴ 540
9
votes
23
replies
8.6k
views
7 follow
Tutorial: OrthoMCL installation on Ubuntu Linux
ubuntu orthomcl mysql linux
updated 18 days ago by 39k • written 5.4 years ago by ▴ 310
9
votes
3
replies
3.9k
views
Tutorial: Ht Sequence Analysis With R And Bioconductor By The Bioinformatics Center At Uc Riverside
bioconductor
updated 3 months ago by 39k • written 10.8 years ago by 98k
9
votes
9
replies
3.7k
views
Tutorial: Determine % of reference genome covered by aligned SAM/BAM
reference-coverage ngs
updated 20 days ago by 39k • written 5.7 years ago by 85k
8
votes
12
replies
6.2k
views
Tutorial: Create your own VPN to access work resources from home
tinyproxy OpenVPN VPN
updated 8 weeks ago by 39k • written 7.0 years ago by 13k
8
votes
3
replies
2.5k
views
Tutorial: Free online interactive Ensembl training
ensembl training genome
updated 10 months ago by 39k • written 7.3 years ago by 23k
8
votes
19
replies
12k
views
9 follow
Tutorial: A:orthomcl with local mysql server on linux server, complete install
mysql orthomcl
updated 12 weeks ago by 39k • written 8.5 years ago by ▴ 580
8
votes
0
replies
2.2k
views
Tutorial: Pipes in R: An introduction and some advanced tips and tricks.
R
2.2 years ago by rpolicastro 12k
8
votes
17
replies
2.4k
views
Tutorial: Simple approach to RNA-seq (T-Bioinfo platform)
alignment next-gen-sequencing RNA-seq
updated 9 months ago by 39k • written 7.6 years ago by ▴ 340
8
votes
2
replies
6.3k
views
Tutorial: Troubleshooting issues with SURPI pipeline for pathogen identification from complex metagenomic NGS data.
metagenomics clinical-genomics
updated 16 months ago by 39k • written 8.6 years ago by 12k
8
votes
9
replies
10k
views
Tutorial: Extracting subset of records from FASTA/FASTQ files based on exact/pattern matches of IDs (ONE-LINERS)
fastq fasta
updated 3 months ago by 39k • written 9.1 years ago by ★ 1.8k
8
votes
1
reply
1.1k
views
Tutorial: Split a 'linearised' (flattened) FASTA sequence into multi-line using AWK
fasta awk
updated 11 weeks ago by 39k • written 2.2 years ago by 85k
8
votes
7
replies
7.8k
views
Tutorial: Getting Cegma/Genewise To Work On Centos, Rhel
centos genewise rhel cegma
updated 16 months ago by 39k • written 9.5 years ago by ★ 2.6k
7
votes
2
replies
1.5k
views
Tutorial: A tale of two heatmap function
clustering heatmap
updated 8 weeks ago by 39k • written 6.7 years ago by ★ 2.9k
7
votes
0
replies
5.1k
views
Tutorial: Mothur Analyzing 16S Of Ngs High Through-Put Sequencing
next-gen
updated 3 months ago by 39k • written 11.0 years ago by ▴ 120
7
votes
3
replies
1.2k
views
Tutorial: Automated dbSNP lookup by rsID position, plus genome build liftover
rsid hg19 liftover hg38 dbsnp
updated 8 weeks ago by ▴ 100 • written 9 months ago by 85k
7
votes
2
replies
3.3k
views
Tutorial: List Of Tools For Mapping High-Throughput Sequencing Data (2012)
next-gen mapping
updated 3 months ago by 39k • written 10.7 years ago by 11k
7
votes
2
replies
1.7k
views
Tutorial: Introduction to Human Genomics for Clinical Informaticists
genome
updated 20 days ago by 39k • written 5.8 years ago by ▴ 90
7
votes
1
reply
2.0k
views
Tutorial: A gentle introduction to biogo
sequence golang biogo
updated 19 days ago by 39k • written 5.6 years ago by ★ 1.7k
7
votes
8
replies
3.0k
views
Tutorial: Determine if a transcription factor is bound with CENTIPEDE
ChIP-Seq transcription-factor DNase-Seq CENTIPEDE
updated 6 months ago by 39k • written 7.9 years ago by ★ 2.2k
7
votes
0
replies
2.8k
views
Tutorial: On the concept of constant or intercept used in Differential Expression (DE) analysis
regression limma DESeq2
updated 8 weeks ago by 39k • written 7.1 years ago by ★ 5.1k
7
votes
14
replies
2.4k
views
6 follow
Tutorial: Install required dependencies for GATK4 on remote server without root privilege
gatk
updated 7 months ago by • 0 • written 15 months ago by ▴ 30
7
votes
2
replies
11k
views
Tutorial: Howto use NCBI programs behind a HTTP proxy
blast-plus HTTP-proxy SRA-toolkit
updated 10 months ago by 39k • written 7.3 years ago by ★ 1.8k
7
votes
0
replies
4.5k
views
Tutorial: How To Perform A Hierarchical Clustering Using Interactive Heatmaps From Gitools?
clustering
updated 3 months ago by 39k • written 9.2 years ago by ▴ 990
6
votes
2
replies
2.5k
views
Tutorial: Tutorial Bioinformatics Static Website
website
updated 3 months ago by 39k • written 9.3 years ago by ▴ 610
6
votes
2
replies
1.1k
views
Tutorial: GSE28955 - Agilent-016436 Human miRNA Microarray 1.0
limma GPL6955 Microarray miRNA Agilent
21 months ago by Kevin Blighe 85k
6
votes
1
reply
2.8k
views
Tutorial: Practical Guidelines for the Comprehensive Analysis of ChIP-seq Data
ChIP-Seq peak-calling sequencing
updated 3 months ago by 39k • written 9.1 years ago by ▴ 220
6
votes
0
replies
3.0k
views
Tutorial: Uc Riverside Bioinformatics Manuals
computing-manuals
updated 3 months ago by 39k • written 11.1 years ago by 26k
358 results • Page 4 of 8
Recent Votes
Answer: Assigned taxonomy after dada2 only "NAs" or "Mitochondria"
Comment: Getting Pairwise Sequence Alignment Score With Biopython
C: How does salmon deal with decoy?
A: How does salmon deal with decoy?
A: How does salmon deal with decoy?
Comment: Italicise annotations with pheatmap
Visualizing Graph Alignment Format via minigraph
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Comment: Help with running ATAC using Encode pipeline by Chris ▴ 100
Sure, here is my json file, I have 8 fastq files: { "atac.title" : “atac)”, "atac.description" : “Encode”, …
Comment: Differential protein expression analysis by dsull ★ 4.2k
Yes, you need to log-transform. I've had a good experience using limma for proteomics analyses (limma uses a moderated t-test).
Answer: Assigned taxonomy after dada2 only "NAs" or "Mitochondria" by mattze731 ▴ 10
Never mind. Someone had put all the 16S files into the ITS folder and vice versa. After using the 16S dada2 pipeline on the actual 16S file…
Comment: Getting Pairwise Sequence Alignment Score With Biopython by Jonathan Lefebre ▴ 70
Dear Alexander, to answer 2) first: This is just a fasta file that you can obtain essentially from every multiple sequence alignment soft…
Comment: Stratified sample assignment for analysis by ATpoint 72k
Batches for what? Processing/sequencing, what data are we talking about? If this is indeed paired then you basically must keep samples of a…
Answer: Visualizing Graph Alignment Format via minigraph by colindaven 4.8k
That's a really good question. Short version: not much to my knowledge, aside from looking at it, or filtering it (as it's a PAF like forma…
Comment: Alignment of case vs. control from different origin by i.sudbery 17k
BTW - Most TCGA cancer types do have normals amoungst the samples.
Comment: Alignment of case vs. control from different origin by i.sudbery 17k
The assumption of these studies is that any batch effect within a batch affects both treatment and control equally, so that when you divide…
Answer: Stratified sample assignment for analysis by Vincent Laufer ★ 2.9k
First, you didn't tell us what kind of data you are working with. For arguments sake, I'll assume bulk RNA-seq. Generally, your options …
Comment: VEP tab/vcf - Different output by Ben_Ensembl ★ 2.2k
You can use the ---show_ref_allele flag when running the VEP query. This will add the reference allele in the output and is mainly useful f…
Comment: Get relationships and hierarchies for GO terms by Alexander ▴ 70
For R-users might be interesting to look at notebook "CAFA5: train set GO terms" https://www.kaggle.com/code/antoninadolgorukova/cafa5-trai…
Comment: Getting Pairwise Sequence Alignment Score With Biopython by Alexander ▴ 70
Thanks for sharing ! Just these days I am trying to wrap my mind on protein alignments. I wonder: 1) "PID" in your post is "percentage o…
Answer: What kind of statistical test does Cellranger count use? by fracarb8 ▴ 950
You should read the [cellranger documentation][1] to understand how the analysis are performed. For example, it uses `graphclust` for clust…
Answer: Gene prediction software by alexandru.bologa.marian ▴ 40
Hi, I don't know if there are tools designed to predict pseudogenes, but If i understand correctly from your post you could predict all th…
Answer: Getting Pairwise Sequence Alignment Score With Biopython by Jonathan Lefebre ▴ 70
Maybe quite late, but in case other people are looking for this. Pairwise sequence identity can be easily calculated using basic python fun…
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