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384 results • Page 3 of 8
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3
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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
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
81
votes
8
replies
8.3k
views
6 follow
Tutorial: Current Topics in Genome Analysis 2014 (collection of educational lectures)
workshop lectures genomics training
updated 9 months ago by 41k • written 9.5 years ago by 19k
14
votes
0
replies
8.2k
views
Tutorial: Video: ChIP-Seq Analysis and Visualization using Galaxy and IGB.
IGB ChIP-Seq Galaxy MACS RNA-Seq
updated 20 months ago by 41k • written 8.9 years ago by ▴ 860
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
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
19
votes
13
replies
8.0k
views
10 follow
Tutorial: Setting up Aspera Connect (ascp) on Linux and macOS
ascp aspera
updated 5 weeks ago by • 0 • written 17 months ago by 78k
0
votes
0
replies
7.9k
views
Tutorial: Multicollinearity VIF (Variance Inflation Factor) Analysis in Panel data EVIEWS 9
R eviews
updated 6 months ago by 41k • written 5.9 years ago by ▴ 10
50
votes
1
reply
7.9k
views
Tutorial: Basic normalization, batch correction and visualization of RNA-seq data
edger RNA-seq
updated 10 months ago by 41k • written 3.2 years ago by 78k
16
votes
11
replies
7.9k
views
Tutorial: How to Use Biostars, Part II: Post types, Deleting, (Un)Subscribing, Linking and Bookmarking
meta how-to documentation
8 months ago by Ram 41k
20
votes
2
replies
7.8k
views
Tutorial: Creating a karyotype plot with genes using karyoploteR
karyoploteR visualization R genome
updated 6 months ago by 41k • written 6.0 years ago by ★ 3.4k
6
votes
1
reply
7.7k
views
Tutorial: Expression Analysis Of Rna-Seq Experiments With Tophat And Cufflinks
tophat RNA-seq cufflinks
updated 9 months ago by 41k • written 11.6 years ago by 99k
12
votes
0
replies
7.6k
views
Tutorial: Plot average methylation levels across TSS region
bedtools RRBS R methylation
updated 20 months ago by 41k • written 8.9 years ago by ★ 4.7k
42
votes
19
replies
7.6k
views
8 follow
Tutorial: Designing Command-Line Interfaces (Clis) For Scientific Software
software
updated 9 months ago by 41k • written 10.8 years ago by 4.1k
26
votes
17
replies
7.4k
views
8 follow
Tutorial: virtualenv - running Python based software in isolation
python virtualenv
updated 15 months ago by 41k • written 9.3 years ago by 6.0k
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
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
60
votes
2
replies
7.2k
views
Tutorial: Table Of Contents To All Review Paper Compilations On Biostar
papers
updated 9 months ago by 41k • written 11.3 years ago by 99k
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
12
votes
11
replies
7.1k
views
Tutorial: How to upload your RNA-Seq data to NCBI Sequence Read Archive (SRA)
NCBI Bioproject SRA BioSample
updated 7 months ago by 41k • written 6.7 years ago by ★ 2.4k
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 11.6 years ago by 99k
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
15
votes
1
reply
6.8k
views
Tutorial: A compilation of conversion tools for BED, SAM/BAM, psl, pslx, blast tabular and blast xml
psl SAM blast BED
updated 6 months ago by 41k • written 6.1 years ago by ★ 3.0k
15
votes
2
replies
6.7k
views
Tutorial: Genotype And Snp Calling Review Papers
snp
updated 9 months ago by 41k • written 11.3 years ago by 99k
2
votes
0
replies
6.7k
views
Tutorial: How to - Install Python packages in a virtual environment (virtualenv)
ubuntu cutadapt virtualenv python windows
updated 6 months ago by 41k • written 6.0 years ago by ▴ 320
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
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
16
votes
0
replies
6.5k
views
Tutorial: Introduction To Ngs Bioinformatics By The Bioinformatics Team At The University Of Texas
course training
updated 9 months ago by 41k • written 11.5 years ago by 99k
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
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
23
votes
19
replies
6.4k
views
10 follow
Tutorial: MutScan: Detect important mutations by scanning FastQ files directly
fastq mutation cancer target
updated 8 months ago by 41k • written 7.2 years ago by ★ 2.5k
21
votes
9
replies
6.4k
views
8 follow
Tutorial: Interactive Perl Learning
perl
updated 9 months ago by 41k • written 10.5 years ago by 9.7k
14
votes
2
replies
6.3k
views
Tutorial: ChIP-seq analysis tutorial
ChIP-Seq
updated 8 months ago by 41k • written 8.3 years ago by ★ 3.6k
21
votes
10
replies
6.3k
views
Tutorial: Finding the significance of the overlap between 2 or more gene sets using simulation in R.
tidyverse gene R
updated 8 months ago by 41k • written 3.3 years ago by 12k
16
votes
9
replies
6.3k
views
Tutorial: TCGA transcriptome data to R (DESeq2)
TCGA GDC DESeq2
updated 18 months ago by ▴ 70 • written 2.0 years ago by ★ 1.3k
6
votes
0
replies
6.2k
views
Tutorial: Leveraging Flow Order And Flow Signals From Ion Torrent Data
ion-torrent
updated 9 months ago by 41k • written 11.6 years ago by ▴ 360
16
votes
6
replies
6.2k
views
Tutorial: How to make your snakefiles self-documenting
snakemake
updated 8 months ago by 41k • written 7.1 years ago by ★ 1.7k
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
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
20
votes
7
replies
6.1k
views
Tutorial: Showing up and down regulated GO and pathway using enrichR and ggplot2
ggplot2 RNA-Seq R
updated 8 months ago by 41k • written 5.2 years ago by ▴ 770
14
votes
7
replies
6.1k
views
Tutorial: Visualization of ChIP-Seq peak overlaps using HOMER mergePeaks and UpSetR
ChIP-Seq peaks R HOMER
updated 8 months ago by 41k • written 7.6 years ago by ★ 3.4k
14
votes
31
replies
6.1k
views
6 follow
Tutorial: gene set filter/selection for training ab initio annotation tools
geneset genome gene abinitio
updated 9 months ago by 41k • written 4.3 years ago by 8.4k
19
votes
7
replies
6.1k
views
Tutorial: scRNA-seq CITE-seq-count bioinformatics
CITE-seq-count scRNA-seq RNA-Seq
updated 4 months ago by 78k • written 3.7 years ago by 5.8k
34
votes
15
replies
6.0k
views
6 follow
Tutorial: How to do data cleaning for VCF genetic file
vcf
updated 8 months ago by 41k • written 4.5 years ago by ★ 9.3k
4
votes
1
reply
6.0k
views
Tutorial: Chip-Seq Data Analysis Tutorial
chip-seq
updated 9 months ago by 41k • written 11.6 years ago by ▴ 360
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
22
votes
2
replies
5.8k
views
Tutorial: Use a workflow management tool to manage your computational pipelines
workflow-management snakemake pipeline
updated 8 months ago by 41k • written 7.1 years ago by ★ 2.1k
18
votes
2
replies
5.8k
views
Tutorial: Update kraken databases
database kraken k-mer python
updated 6 months ago by 41k • written 6.6 years ago by 5.3k
13
votes
6
replies
5.7k
views
Tutorial: Trim & align paired-end reads in a single pass
align trim fastq pipe paired-end
updated 8 months ago by 41k • written 7.5 years ago by 14k
13
votes
7
replies
5.6k
views
Tutorial: STARsolo config for 10x Chromium v1, v2, v3
Chromium 10x STARsolo STAR
updated 8 months ago by 41k • written 3.2 years ago by 86k
384 results • Page 3 of 8
Recent Votes
Comment: gatk SelectVariants is giving dupilicate allele error while extracting SNPs out
Answer: How to query 1000 genomes project VCF files for specific regions without downloa
Answer: Issue softclipping reads when they belong and don't belong to a common amplicon
Answer: Issue softclipping reads when they belong and don't belong to a common amplicon
Answer: how to remove multiple columns from a file in R
Answer: how to remove multiple columns from a file in R
Answer: Read count vs Depth
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Recent Replies
Comment: Normalization of RNA captureSeq data (<20 genes captured) by ATpoint 78k
What is the question exactly? With only 20 genes you basically **must** use the spike-ins as that few genes do not really allow to normaliz…
Comment: Building reference dbSNP file using WGS samples by analyst ▴ 10
Dear [Brian][1] I realized that problem is with callvariants.sh script because when I called variants using freebayes I did not find aforem…
Comment: gatk SelectVariants is giving dupilicate allele error while extracting SNPs out by analyst ▴ 10
Its bbmap tool callvariants.sh. I think you are right because I did not get such error when I called variants through freebayes.
Answer: Efficient way of calculating the number of mismatches between two sets of sequen by j.gleixner • 0
Since all your sequences have the same length (say M) and you are only looking concerned with hamming distance you can encode your sequence…
Comment: Where to download excel file to include major human disease, prevalence and inci by GenoMax 136k
ChatGPT says Disease Prevalence Approximate Number of Cases (Worldwide) Cardiovascular Diseases High Over 17 million deaths annual…
Comment: Where to download excel file to include major human disease, prevalence and inci by Pierre Lindenbaum 158k
using wikidata: https://query.wikidata.org/sparql?query=%0ASELECT%20%3Fitem%20%3FitemLabel%20%3FitemDescription%20%3Fprevalence%20%3Fdoid%0…
Comment: Opinion on miRNA pipeline by ju_ra • 0
Thank you very much! I see you decided to go for Bowtie as aligner. Do you see any issue in using STAR (as a splice aware reader technicall…
Answer: How to avoid missannotated GO terms? by Elisabeth Gasteiger ★ 2.3k
Please contact the UniProt helpdesk whenever you find such annotations, especially in these cases where the GO evidence/source tag says "Un…
Comment: gatk SelectVariants is giving dupilicate allele error while extracting SNPs out by Pierre Lindenbaum 158k
again, it's a problem with the variant caller, which is ?
Comment: gatk SelectVariants is giving dupilicate allele error while extracting SNPs out by analyst ▴ 10
Not only opposite case but same case nucleotides are also present in vcf fle. ![enter image description here][1] [1]: /media/images/4…
Comment: gatk SelectVariants is giving dupilicate allele error while extracting SNPs out by analyst ▴ 10
Yes [Pierre][1] there is lower case **g** in **REF** and upper case **G** in **ALT** field. My question is that why variant caller is calli…
Answer: gatk SelectVariants is giving error while extracting SNPs out of vcf file by Pierre Lindenbaum 158k
This is an error in your input vcf file. The REF allele MUST be différent from the ALT allele.
Comment: gatk SelectVariants is giving error while extracting SNPs out of vcf file by analyst ▴ 10
I observed that my reference genomic fasta file contains both lower case and upper case nucleotides. Do I need to convert lower case nucle…
Comment: Building reference dbSNP file using WGS samples by analyst ▴ 10
I observed that both lower and upper cases are present in reference fasta file. Is bbtool case sensitive that while calling variants it con…
Comment: Read count vs Depth by Mary • 0
Thanks Brain Bushnell Referring to my query1: So u mean that for a particular gene, if total read count is 6, then depth may be just 1 or …
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