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Tutorial: [[ Please read before posting a question ::: How To Ask A Good Question ]]
how-to
updated 8 months ago by 41k • written 4.9 years ago by 78k
49
votes
7
replies
11k
views
7 follow
Tutorial: Genome Assembly Review Papers
assembly papers
updated 9 months ago by 41k • written 11.3 years ago by 99k
48
votes
30
replies
9.4k
views
11 follow
Tutorial: How to Use Biostars, Part-I: Questions, Answers, Comments and Replies
documentation meta how-to
updated 5 weeks ago by 78k • written 7.8 years ago by 41k
47
votes
19
replies
13k
views
8 follow
Tutorial: Fastq Quality Control And Reporting - Aka Fastqc Versus The New Contenders
quality-control fastqc
updated 11 months ago by 41k • written 10.8 years ago by 99k
45
votes
2
replies
36k
views
Tutorial: Mapping Reads With Bwa And Bowtie
bowtie bwa
updated 9 months ago by 41k • written 11.7 years ago by ▴ 540
44
votes
3
replies
12k
views
Tutorial: A Wet-Lab Guide to 'what I wish I had known' for Computational Biology
bioinformatics computational-biology
updated 8 months ago by 41k • written 7.7 years ago by ★ 3.2k
44
votes
6
replies
23k
views
Tutorial: Greatly speed up conda by using mamba
software
updated 22 months ago by ▴ 40 • written 2.7 years ago by 12k
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
42
votes
16
replies
23k
views
15 follow
Tutorial: Tutorial: Analyze exome Copy number variation (CNV) in single patient or in population.
GISTIC varscan2 CNV copy-number
updated 16 months ago by 41k • written 8.2 years ago by ★ 2.4k
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
42
votes
2
replies
18k
views
Tutorial: Sequencing Technology Review Papers
sequencing papers
updated 9 months ago by 41k • written 11.3 years ago by 99k
40
votes
9
replies
11k
views
10 follow
Tutorial: Resources for flow cytometry bioinformatics
single-cell flow-cytometry
updated 9 months ago by 41k • written 9.7 years ago by ★ 1.9k
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
39
votes
8
replies
12k
views
10 follow
Tutorial: Methylation Analysis Tutorial in R_part1
cancer R methylation
updated 9 months ago by 41k • written 3.2 years ago by 3.1k
36
votes
14
replies
32k
views
14 follow
Tutorial: installing samtools with conda - overcoming two common errors
samtools conda
updated 4 weeks ago by ▴ 50 • written 3.3 years ago by ▴ 160
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
35
votes
17
replies
16k
views
12 follow
Tutorial: Machine Learning For Cancer Classification - Part 3 - Predicting With A Random Forest Classifier
machine-learning classification
updated 7 months ago by 136k • written 10.0 years ago by 20k
34
votes
15
replies
19k
views
12 follow
Tutorial: TCGA UUIDS to TCGA barcode (SampleID) in R
next-gen GDC R TCGA
updated 8 months ago by 41k • written 7.2 years ago by ▴ 310
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
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
32
votes
12
replies
29k
views
7 follow
Tutorial: So What Does The Sequence Duplication Rate Really Mean In A Fastqc Report
quality-control fastqc
updated 9 months ago by 41k • written 10.1 years ago by 99k
31
votes
6
replies
11k
views
Tutorial: A simple tutorial for a complex ComplexHeatmap
clustering pam arthritis ComplexHeatmap
updated 8 months ago by 41k • written 3.6 years ago by 86k
31
votes
8
replies
11k
views
7 follow
Tutorial: How To Create A Bioinformatics Pipeline Using Spotify !
python pipeline
updated 9 months ago by 41k • written 9.7 years ago by ▴ 810
30
votes
14
replies
16k
views
8 follow
Tutorial: Installation of the MuSiC suite on unsupported Linux distributions
genome-music linux smg
updated 9 months ago by 41k • written 10.8 years ago by 6.0k
30
votes
6
replies
22k
views
Tutorial: Transforming And Manipulating Color Space Reads
conversion solid
updated 14 months ago by 41k • written 11.6 years ago by 99k
29
votes
10
replies
73k
views
9 follow
Tutorial: Installing an updated R version (>=4.0) using conda
software-error R
updated 9 months ago by 41k • written 2.7 years ago by ★ 1.5k
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
28
votes
13
replies
12k
views
9 follow
Tutorial: How to get FASTQ reads from the Short Read Archive (SRA)
fastq sra
updated 22 months ago by ★ 1.3k • written 2.1 years ago by 99k
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
27
votes
0
replies
3.4k
views
Tutorial: Building Docker images
singularity docker container
16 months ago by ATpoint 78k
26
votes
0
replies
2.3k
views
Tutorial: Resources / databases for clinical interpretation of cancer variants
interpretation cancer annotation variant
updated 8 months ago by 41k • written 4.1 years ago by 19k
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
25
votes
15
replies
8.6k
views
8 follow
Tutorial: Syllabus To Learn Bioinformatics From Online Video Resources
course training mooc
updated 9 months ago by 41k • written 10.9 years ago by 9.7k
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
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
23
votes
8
replies
5.2k
views
Tutorial: A Practical (And Opinionated) Guide To Analyzing Human Methylation 450K Data
450K methylation
updated 23 months ago by 41k • written 9.3 years ago by 24k
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
22
votes
1
reply
3.1k
views
Tutorial: Introduction To R Course Materials Available
R
updated 11 months ago by 41k • written 11.6 years ago by 26k
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
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
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
21
votes
2
replies
5.2k
views
Tutorial: Extracting genomic feature sequences from GTF/GFF files with AGAT
extract GTF GFF sequence
updated 15 months ago by ▴ 40 • written 2.6 years ago by 8.4k
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
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
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
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
20
votes
0
replies
8.6k
views
Tutorial: Metagenomics Review Papers
metagenomics papers
updated 9 months ago by 41k • written 11.3 years ago by 99k
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
20
votes
14
replies
3.7k
views
Tutorial: Video-tutorials: How to get started using EaSeq for interactive ChIP-seq data visualization and exploration (Windows)
ChIP-Seq visualization Windows EaSeq
updated 8 months ago by 41k • written 7.6 years ago by ▴ 460
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
384 results • Page 2 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: SQL request from NCBI metadata and stat_analysis tables by marie.harmel • 0
Thank you for your answer but unfortunately I tried it and it makes the same kind of ouptut as mine, with multtiple new (false) lines (spl…
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…
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