Limit : all time
all time today this week this month this year
379 results • Page 3 of 8
Sort: Rank
Rank Views Votes Replies
21
votes
10
replies
6.0k
views
Tutorial: Finding the significance of the overlap between 2 or more gene sets using simulation in R.
tidyverse gene R
updated 6 months ago by 40k • written 3.1 years ago by 12k
12
votes
2
replies
1.2k
views
Tutorial: Factors in R - How do they work, and how did I break my data?
R
updated 6 months ago by 40k • written 2.5 years ago by 12k
149
votes
35
replies
60k
views
33 follow
Tutorial: Tools For Metagenomic Data Analysis
metagenomics next-gen
updated 7 months ago by 40k • written 10.8 years ago by ★ 1.6k
15
votes
2
replies
3.4k
views
Tutorial: Methylation Analysis Tutorial in R_part2
cancer methylation RNA-Seq R
updated 6 months ago by 40k • written 3.0 years ago by 3.0k
16
votes
7
replies
14k
views
Tutorial: Integrating VDJ sequencing data with Seurat
VDJ Seurat sc-RNAseq clonotyping
updated 6 months ago by 40k • written 4.3 years ago by ▴ 310
288
votes
33
replies
99k
views
25 follow
Tutorial: Cheat Sheet For One-Based Vs Zero-Based Coordinate Systems
coordinates
updated 7 months ago by 40k • written 9.9 years ago by 20k
5
votes
0
replies
4.1k
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 6 months ago by 40k • written 2.7 years ago by 134k
11
votes
0
replies
5.8k
views
Tutorial: Yes .. BBMap can do that! - Part II randomreads (read simulation), demuxbyname/filterbyname, bbsplit (read binning/decontamination) and pileup (cover…
bbmap
updated 6 months ago by 40k • written 2.7 years ago by 134k
10
votes
0
replies
3.8k
views
Tutorial: Yes .. BBMap can do that! - Part I : bbmap (aligner), bbduk (scan/trim), repair (fix PE reads) and reformat (format conversions)
bbmap
updated 6 months ago by 40k • written 2.7 years ago by 134k
11
votes
1
reply
2.5k
views
Tutorial: Guidelines for the computational analysis of single-cell RNA sequencing data
scRNA-seq
updated 6 months ago by 40k • written 2.7 years ago by ★ 25k
40
votes
9
replies
11k
views
10 follow
Tutorial: Resources for flow cytometry bioinformatics
single-cell flow-cytometry
updated 6 months ago by 40k • written 9.5 years ago by ★ 1.9k
0
votes
1
reply
2.7k
views
Tutorial: Getting the lineage of an organism from NCBI taxonomy data
biosql python taxonomy
updated 6 months ago by 40k • written 5.2 years ago by ▴ 310
76
votes
13
replies
15k
views
12 follow
Tutorial: Exploring cancer mutation data portals
TCGA Cancer ICGC Data-Portal Mutation
updated 23 months ago by 40k • written 9.3 years ago by 19k
6
votes
10
replies
4.8k
views
Tutorial: Differentially methylated regions: Easy & Fast Identification and ANnoTation
DMR dna-methylation
updated 6 months ago by 40k • written 5.6 years ago by ▴ 370
43
votes
6
replies
12k
views
Tutorial: Annotating TCGA MAFs with the latest Ensembl/Gencode transcripts
ensembl maf tcga vcf
updated 7 months ago by 40k • written 9.7 years ago by 6.0k
5
votes
3
replies
5.0k
views
Tutorial: bam2rpkm by bedtools
bam RNA-Seq bedtools rpkm
updated 6 months ago by • 0 • written 5.9 years ago by ▴ 130
16
votes
11
replies
7.7k
views
Tutorial: How to Use Biostars, Part II: Post types, Deleting, (Un)Subscribing, Linking and Bookmarking
meta how-to documentation
6 months ago by Ram 40k
48
votes
28
replies
8.6k
views
9 follow
Tutorial: How to Use Biostars, Part-I: Questions, Answers, Comments and Replies
documentation meta how-to
4 months ago by Ram 40k
104
votes
6
replies
24k
views
6 follow
Tutorial: Creating workflows with snakemake and conda
workflow snakemake conda
updated 6 months ago by 40k • written 5.1 years ago by 16k
18
votes
40
replies
17k
views
16 follow
Tutorial: Easy way to run easily orthoMCL (Copy & paste)
all-v-all orthomcl
updated 6 months ago by 40k • written 7.3 years ago by ▴ 170
24
votes
4
replies
6.9k
views
Tutorial: Using EnrichedHeatmap for visualization of NGS experiments
heatmap chip-seq atac-seq EnrichedHeatmap
updated 6 months ago by 40k • written 4.1 years ago by 77k
15
votes
4
replies
4.3k
views
Tutorial: RNASeq tutorial for gene differential expression analysis
Transcriptomics bioconductor RNA-Seq R
updated 6 months ago by 40k • written 3.2 years ago by ▴ 330
26
votes
0
replies
2.3k
views
Tutorial: Resources / databases for clinical interpretation of cancer variants
interpretation cancer annotation variant
updated 6 months ago by 40k • written 4.0 years ago by 19k
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 6 months ago by 40k • written 3.5 years ago by ★ 2.4k
60
votes
52
replies
41k
views
23 follow
Tutorial: Creating Interactive Volcano Plots with R and Plot.ly
plotly R volcano-plot
updated 6 months ago by 40k • written 7.0 years ago by ★ 3.3k
12
votes
7
replies
5.4k
views
Tutorial: STARsolo config for 10x Chromium v1, v2, v3
Chromium 10x STARsolo STAR
updated 6 months ago by 40k • written 3.0 years ago by 86k
18
votes
22
replies
8.1k
views
10 follow
Tutorial: Create de novo repeat library
de-novo repeat annotation
updated 8 days ago by ▴ 20 • written 3.8 years ago by 8.2k
0
votes
0
replies
978
views
Tutorial: BrainArray CDF, annotation, etc
db brainarray cdf
updated 6 months ago by 40k • written 3.0 years ago by 86k
12
votes
0
replies
2.4k
views
Tutorial: Long versus wide data for plotting genomics data in R.
ggplot2 tidyverse data.table R
updated 6 months ago by 40k • written 3.1 years ago by 12k
76
votes
70
replies
17k
views
18 follow
Tutorial: Clustering of DAVID gene enrichment results from gene expression studies
enrichment david
updated 6 months ago by 40k • written 5.6 years ago by 86k
1
vote
1
reply
1.2k
views
Tutorial: Downloading GnuWin and using to convert txt to bed file for windows users
bed bed2txt sequencing txt
updated 6 months ago by 40k • written 3.1 years ago by • 0
4
votes
3
replies
4.3k
views
Tutorial: How to get full taxonomy classification using taxize and myTAI
taxonomy R
updated 6 months ago by 40k • written 5.5 years ago by ★ 3.9k
4
votes
1
reply
1.2k
views
Tutorial: Real World BEDtools. Practical Examples for Variant Filtering and Gene Annotations
BED BEDtools
updated 6 months ago by 40k • written 3.2 years ago by ▴ 40
3
votes
0
replies
3.3k
views
Tutorial: Sorting GFF/GTF files
gtf gff
updated 6 months ago by 40k • written 3.2 years ago by 8.2k
20
votes
6
replies
5.2k
views
Tutorial: Open Targets and programmatic access
open-targets disease API drug
updated 6 months ago by 40k • written 7.0 years ago by ★ 5.2k
2
votes
2
replies
1.8k
views
Tutorial: Human mitochondrial DNA annotation in SnpEff
chrMT SNP snpEff
updated 6 months ago by 40k • written 3.3 years ago by 3.2k
12
votes
5
replies
2.1k
views
Tutorial: FASTA file split
fasta
updated 6 months ago by 40k • written 3.3 years ago by 8.2k
0
votes
0
replies
1.5k
views
Tutorial: VIDEO: Installing BLAST Databases on Your Own Computer
BLAST-databases Linux sequence MacOSX
updated 6 months ago by 40k • written 3.3 years ago by ▴ 450
0
votes
0
replies
895
views
Tutorial: VIDEO: BLAST Searches Through a Data Science Lens
Covid19 Data-Science sequence BLAST
updated 6 months ago by 40k • written 3.3 years ago by ▴ 450
2
votes
1
reply
1.4k
views
Tutorial: A very simple way to detect viruses and microorganisms from mNGS FASTQ data using fastv
SARS-CoV-2 fastv COVID-19 viruses
updated 6 months ago by 40k • written 3.4 years ago by ★ 2.4k
71
votes
26
replies
26k
views
15 follow
Tutorial: How To Separate Illumina Based Strand Specific Rna-Seq Alignments By Strand
RNA-seq
updated 7 months ago by 40k • written 9.6 years ago by 98k
59
votes
43
replies
19k
views
18 follow
Tutorial: Polish PacBio assembly with latest PacBio tools : an affordable solution for everyone
pbalign pacbio arrow smrt-limk
updated 6 months ago by 40k • written 6.0 years ago by ★ 1.4k
20
votes
7
replies
6.0k
views
Tutorial: Showing up and down regulated GO and pathway using enrichR and ggplot2
ggplot2 RNA-Seq R
updated 6 months ago by 40k • written 5.0 years ago by ▴ 760
4
votes
0
replies
1.6k
views
Tutorial: NIH CDE browser for TCGA clinical data CDE codes
nih tcga metadata cde
updated 6 months ago by 40k • written 3.5 years ago by 86k
10
votes
4
replies
10k
views
Tutorial: Using the MinION MinKNOW software on Ubuntu 1604
long-reads oxford-nanopore minion
updated 6 months ago by 40k • written 4.2 years ago by 5.5k
0
votes
0
replies
1.1k
views
Tutorial: Training GeneMark-EP+ ab-initio tool
abinitio training genemark annotation
updated 6 months ago by 40k • written 3.7 years ago by 8.2k
2
votes
1
reply
2.8k
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 6 months ago by 40k • written 3.6 years ago by ▴ 10
5
votes
0
replies
3.0k
views
Tutorial: How to run CWL with Nextflow
cwl nextflow
updated 6 months ago by 40k • written 3.6 years ago by ★ 3.3k
5
votes
2
replies
2.1k
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 6 months ago by 40k • written 4.7 years ago by ▴ 10
50
votes
3
replies
4.4k
views
Tutorial: [[ Please read before posting a question ::: How To Ask A Good Question ]]
how-to
updated 6 months ago by 40k • written 4.7 years ago by 77k
379 results • Page 3 of 8
Recent Votes
A: .gstmp extension on .bam files downloaded from google bucket; and EOF marker is
Comment: Significance testing of top vs. random SNPs
Answer: Search RCSB with a list of protein names?
A: running RAxML and MrBayes over concatinated multiple sequence alignments
Comment: Weirdness in annotation (missing allele frequencies)
Comment: Weirdness in annotation (missing allele frequencies)
Comment: ncbi error report log for validate fastq issue
Recent Locations • All
Japan, 3 minutes ago
United States, 9 minutes ago
United States, 17 minutes ago
Seattle, WA USA, 23 minutes ago
Pakistan, 25 minutes ago
China, 28 minutes ago
India, 38 minutes ago
Recent Awards • All
Commentator to dsull ★ 4.8k
Scholar to liorglic ★ 1.3k
Popular Question to natasha.sernova ★ 3.9k
Popular Question to ntsopoul ▴ 50
Teacher to benformatics 3.8k
Popular Question to iislam • 0
Scholar to ATpoint 77k
Recent Replies
Comment: Getting the overlap between two GTF files by Alex Reynolds 35k
What would that be?
Answer: Encountering Error while Running 'make vcf' in Biostar Handbook by Tully • 0
@ialbert ,I am deeply immersed in the fog and request the help ,please
Comment: bedtools intersect by position & stand not working even with common regions by rfran010 ▴ 830
are you sure bedtools can handle the non-standard location of strand information?
Answer: Getting the overlap between two GTF files by rfran010 ▴ 830
Maybe somebody knows something I don't, but I feel like bedtools should be able to handle your gtf files directly. If it's not done alre…
Answer: vcf.gz to vcf by Mark ★ 1.3k
As the error says, the file is not compressed. In linux the file extension is essentially optional. The file could be named `my.vcf.txt` ye…
Answer: Search RCSB with a list of protein names? by Jiyao Wang ▴ 340
You can use NCBI esearch to search the protein names against the structure database to get the PDB IDs, then retrieve the structures.
Answer: How to get ncol = nrow? by Mark ★ 1.3k
Without your actual data, it's hard to assist. I think what you're asking is 'how do I rename the rows of my dataframe(s)'. Taking the …
Comment: MAKER: WARNING: Could not get initialization lock. Trying Again... by GenoMax 134k
What kind of hardware are you running this on? You need to have the right kind of hardware (multiple CPU's not just cores), MPI libraries a…
Answer: Getting the overlap between two GTF files by Alex Reynolds 35k
Using `bedops --intersect` and `gtf2bed` will get their common genomic space: ``` bedops --intersect <(gtf2bed < transcripts.gtf) <(gtf2be…
Comment: Encountering Error while Running 'make vcf' in Biostar Handbook by Tully • 0
```bash # Obtain the makefile curl -s http://data.biostarhandbook.com/make/snpcall.mk > Makefile # Run the makefile make vcf ``` Error me…
Comment: Encountering Error while Running 'make vcf' in Biostar Handbook by Tully • 0
> System Information: Ubuntu 22.04 (WSL2) > > Shell: zsh > > Installation Verification: Yes, doctor.py OK [1]: https://www.biostarhand…
Comment: Retrieve The Reads And Fastq From Bam File by Reem • 0
Did it affect the bamtofastq output file? if so how did you solve the problem? Thanks
Answer: How to import bigwig files into igvR by Trivas ★ 1.5k
You could try seeing if this fixes your issue with rtracklayer: https://support.bioconductor.org/p/p133244/
Comment: Weirdness in annotation (missing allele frequencies) by Jeremy Leipzig 21k
0.60625 is 97/160 so if you have 80 individuals in your VCF that's an internal allele frequency, not gnomAD
Comment: Weirdness in annotation (missing allele frequencies) by Can Abdullah • 0
Yes, I was confused as well. I think the same. Maybe Annovar uses some other resources besides gnomad, but it does not make sense. Also, I …
Traffic: 1283 users visited in the last hour
Content Search
Users
Tags
Badges
Help About
FAQ
Access RSS
API
Stats

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.

Powered by the version 2.3.6