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412 results • Page
3 of 9
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Views
Votes
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3
votes
3
replies
8.8k
views
Tutorial:
High Speed Downloading of SRA, SAM and Fastq Files
fastq
sam
Aspera-Connect
sra
updated 12 months ago by
Ram
43k • written 6.4 years ago by
Wenhu_Cao
▴ 100
20
votes
0
replies
8.8k
views
Tutorial:
Metagenomics Review Papers
metagenomics
papers
updated 15 months ago by
Ram
43k • written 11.7 years ago by
Istvan Albert
100k
9
votes
0
replies
8.7k
views
Tutorial:
Installing And Running Ncbi Blast
blast
updated 15 months ago by
Ram
43k • written 12.1 years ago by
MSU course 2011
▴ 540
81
votes
8
replies
8.6k
views
6 follow
Tutorial:
Current Topics in Genome Analysis 2014 (collection of educational lectures)
workshop
lectures
genomics
training
updated 14 months ago by
Ram
43k • written 9.9 years ago by
Malachi Griffith
20k
20
votes
4
replies
8.6k
views
Tutorial:
DE analysis by edgeR
RNA-Seq
R
edgeR
updated 13 months ago by
Ram
43k • written 7.7 years ago by
zizigolu
★ 4.3k
8
votes
7
replies
8.4k
views
Tutorial:
Getting Cegma/Genewise To Work On Centos, Rhel
centos
genewise
rhel
cegma
updated 2.3 years ago by
Ram
43k • written 10.5 years ago by
Adrian Pelin
★ 2.6k
12
votes
5
replies
8.4k
views
Tutorial:
How To Install BioPerl Without Root Privileges in Ubuntu/Linxu
bioperl
updated 13 months ago by
Ram
43k • written 8.0 years ago by
Shicheng Guo
★ 9.4k
14
votes
0
replies
8.4k
views
Tutorial:
Video: ChIP-Seq Analysis and Visualization using Galaxy and IGB.
IGB
ChIP-Seq
Galaxy
MACS
RNA-Seq
updated 2.1 years ago by
Ram
43k • written 9.3 years ago by
Nowlan Freese
▴ 860
16
votes
11
replies
8.3k
views
Tutorial:
How to Use Biostars, Part II: Post types, Deleting, (Un)Subscribing, Linking and Bookmarking
meta
how-to
documentation
14 months ago by
Ram
43k
20
votes
2
replies
8.1k
views
Tutorial:
Creating a karyotype plot with genes using karyoploteR
karyoploteR
visualization
R
genome
updated 12 months ago by
Ram
43k • written 6.5 years ago by
bernatgel
★ 3.4k
0
votes
0
replies
8.1k
views
Tutorial:
Multicollinearity VIF (Variance Inflation Factor) Analysis in Panel data EVIEWS 9
R
eviews
updated 12 months ago by
Ram
43k • written 6.3 years ago by
helgasaraswati
▴ 10
32
votes
4
replies
8.0k
views
Tutorial:
Fast LD computation from VCF files using tomahawk
ld
snp
vcf
vcftools
bcftools
updated 14 months ago by
Ram
43k • written 5.5 years ago by
firestar
★ 1.6k
42
votes
19
replies
7.9k
views
8 follow
Tutorial:
Designing Command-Line Interfaces (Clis) For Scientific Software
software
updated 14 months ago by
Ram
43k • written 11.2 years ago by
Daniel Standage
4.1k
12
votes
0
replies
7.9k
views
Tutorial:
Plot average methylation levels across TSS region
bedtools
RRBS
R
methylation
updated 2.1 years ago by
Ram
43k • written 9.3 years ago by
TriS
★ 4.7k
6
votes
1
reply
7.8k
views
Tutorial:
Expression Analysis Of Rna-Seq Experiments With Tophat And Cufflinks
tophat
RNA-seq
cufflinks
updated 15 months ago by
Ram
43k • written 12.0 years ago by
Istvan Albert
100k
26
votes
17
replies
7.8k
views
8 follow
Tutorial:
virtualenv - running Python based software in isolation
python
virtualenv
updated 20 months ago by
Ram
43k • written 9.8 years ago by
Ian
6.0k
24
votes
4
replies
7.7k
views
Tutorial:
Using EnrichedHeatmap for visualization of NGS experiments
heatmap
chip-seq
atac-seq
EnrichedHeatmap
updated 14 months ago by
Ram
43k • written 4.8 years ago by
ATpoint
82k
12
votes
11
replies
7.6k
views
Tutorial:
How to upload your RNA-Seq data to NCBI Sequence Read Archive (SRA)
NCBI
Bioproject
SRA
BioSample
updated 12 months ago by
Ram
43k • written 7.2 years ago by
CandiceChuDVM
★ 2.4k
6
votes
4
replies
7.5k
views
Tutorial:
Overlay Multiple Tracks In Ucsc Browser [Quick Minimal Tutorial]
visualization
ChIP-seq
RNA-seq
ucsc-genome-browser
bigwig
updated 14 months ago by
Ram
43k • written 11.2 years ago by
Sukhi Singh
11k
60
votes
2
replies
7.4k
views
Tutorial:
Table Of Contents To All Review Paper Compilations On Biostar
papers
updated 15 months ago by
Ram
43k • written 11.7 years ago by
Istvan Albert
100k
64
votes
5
replies
7.3k
views
10 follow
Tutorial:
Informatics of RNA-Seq.
next-gen
RNA-Seq
updated 19 months ago by
Ram
43k • written 8.8 years ago by
GouthamAtla
12k
4
votes
2
replies
7.2k
views
Tutorial:
Analyzing Genomewide Association Study Data: A Tutorial Using Plink
plink
gwas
updated 15 months ago by
Ram
43k • written 12.0 years ago by
Istvan Albert
100k
15
votes
1
reply
7.2k
views
Tutorial:
A compilation of conversion tools for BED, SAM/BAM, psl, pslx, blast tabular and blast xml
psl
SAM
blast
BED
updated 12 months ago by
Ram
43k • written 6.5 years ago by
Joseph Hughes
★ 3.0k
16
votes
9
replies
7.2k
views
Tutorial:
TCGA transcriptome data to R (DESeq2)
TCGA
GDC
DESeq2
updated 23 months ago by
dk0319
▴ 70 • written 2.5 years ago by
Barry Digby
★ 1.3k
22
votes
10
replies
7.1k
views
Tutorial:
Finding the significance of the overlap between 2 or more gene sets using simulation in R.
tidyverse
gene
R
updated 14 months ago by
Ram
43k • written 3.7 years ago by
rpolicastro
13k
6
votes
5
replies
7.0k
views
Tutorial:
use firehose_get to download TCGA data
tcga
RNA-Seq
updated 12 months ago by
Ram
43k • written 6.5 years ago by
jmzeng1314
▴ 140
23
votes
19
replies
6.9k
views
10 follow
Tutorial:
MutScan: Detect important mutations by scanning FastQ files directly
fastq
mutation
cancer
target
updated 13 months ago by
Ram
43k • written 7.6 years ago by
chen
★ 2.5k
2
votes
0
replies
6.9k
views
Tutorial:
How to - Install Python packages in a virtual environment (virtualenv)
ubuntu
cutadapt
virtualenv
python
windows
updated 12 months ago by
Ram
43k • written 6.4 years ago by
vimalkvn
▴ 320
11
votes
0
replies
6.9k
views
Tutorial:
Yes .. BBMap can do that! - Part II randomreads (read simulation), demuxbyname/filterbyname, bbsplit (read binning/decontamination) and pileup (cover…
bbmap
updated 14 months ago by
Ram
43k • written 3.4 years ago by
GenoMax
142k
15
votes
2
replies
6.9k
views
Tutorial:
Genotype And Snp Calling Review Papers
snp
updated 15 months ago by
Ram
43k • written 11.7 years ago by
Istvan Albert
100k
14
votes
31
replies
6.9k
views
6 follow
Tutorial:
gene set filter/selection for training ab initio annotation tools
geneset
genome
gene
abinitio
updated 14 months ago by
Ram
43k • written 4.8 years ago by
Juke34
8.6k
21
votes
5
replies
6.8k
views
Tutorial:
Analysis of single-cell RNA-seq data
single-cell
RNA-Seq
updated 13 months ago by
Ram
43k • written 7.9 years ago by
Geparada
★ 1.5k
8
votes
12
replies
6.8k
views
Tutorial:
Create your own VPN to access work resources from home
tinyproxy
OpenVPN
VPN
updated 13 months ago by
Ram
43k • written 8.0 years ago by
John
13k
19
votes
7
replies
6.6k
views
Tutorial:
scRNA-seq CITE-seq-count bioinformatics
CITE-seq-count
scRNA-seq
RNA-Seq
updated 10 months ago by
ATpoint
82k • written 4.1 years ago by
colindaven
6.4k
17
votes
0
replies
6.6k
views
Tutorial:
Introduction To Ngs Bioinformatics By The Bioinformatics Team At The University Of Texas
course
training
updated 15 months ago by
Ram
43k • written 11.9 years ago by
Istvan Albert
100k
8
votes
2
replies
6.6k
views
Tutorial:
Troubleshooting issues with SURPI pipeline for pathogen identification from complex metagenomic NGS data.
metagenomics
clinical-genomics
updated 2.3 years ago by
Ram
43k • written 9.5 years ago by
GouthamAtla
12k
21
votes
9
replies
6.6k
views
8 follow
Tutorial:
Interactive Perl Learning
perl
updated 14 months ago by
Ram
43k • written 10.9 years ago by
Medhat
9.7k
34
votes
15
replies
6.6k
views
6 follow
Tutorial:
How to do data cleaning for VCF genetic file
vcf
updated 14 months ago by
Ram
43k • written 4.9 years ago by
Shicheng Guo
★ 9.4k
15
votes
7
replies
6.5k
views
Tutorial:
Visualization of ChIP-Seq peak overlaps using HOMER mergePeaks and UpSetR
ChIP-Seq
peaks
R
HOMER
updated 14 months ago by
Ram
43k • written 8.0 years ago by
steve
★ 3.5k
14
votes
2
replies
6.5k
views
Tutorial:
ChIP-seq analysis tutorial
ChIP-Seq
updated 13 months ago by
Ram
43k • written 8.7 years ago by
Ming Tommy Tang
★ 3.9k
16
votes
6
replies
6.5k
views
Tutorial:
How to make your snakefiles self-documenting
snakemake
updated 13 months ago by
Ram
43k • written 7.5 years ago by
Botond Sipos
★ 1.7k
6
votes
0
replies
6.4k
views
Tutorial:
Leveraging Flow Order And Flow Signals From Ion Torrent Data
ion-torrent
updated 15 months ago by
Ram
43k • written 12.0 years ago by
Biostar User
▴ 360
20
votes
7
replies
6.4k
views
Tutorial:
Showing up and down regulated GO and pathway using enrichR and ggplot2
ggplot2
RNA-Seq
R
updated 14 months ago by
Ram
43k • written 5.6 years ago by
ahmad mousavi
▴ 800
29
votes
5
replies
6.4k
views
Tutorial:
Gnu Parallel Tutorial
parallel
gnu-parallel
updated 14 months ago by
Ram
43k • written 10.7 years ago by
ole.tange
★ 4.4k
13
votes
7
replies
6.3k
views
Tutorial:
STARsolo config for 10x Chromium v1, v2, v3
Chromium
10x
STARsolo
STAR
updated 14 months ago by
Ram
43k • written 3.7 years ago by
Kevin Blighe
88k
37
votes
5
replies
6.1k
views
Tutorial:
[Beginner] Introduction to bioinformatics file types
fastq
fasta
bed
SAM
updated 8 months ago by
gallardodiazmiriam
▴ 20 • written 8.8 years ago by
Luke Crichton
▴ 430
4
votes
1
reply
6.1k
views
Tutorial:
Chip-Seq Data Analysis Tutorial
chip-seq
updated 15 months ago by
Ram
43k • written 12.0 years ago by
Biostar User
▴ 360
22
votes
2
replies
6.0k
views
Tutorial:
Use a workflow management tool to manage your computational pipelines
workflow-management
snakemake
pipeline
updated 13 months ago by
Ram
43k • written 7.5 years ago by
Eric Lim
★ 2.1k
13
votes
6
replies
6.0k
views
Tutorial:
Trim & align paired-end reads in a single pass
align
trim
fastq
pipe
paired-end
updated 13 months ago by
Ram
43k • written 7.9 years ago by
dariober
14k
18
votes
2
replies
5.9k
views
Tutorial:
Update kraken databases
database
kraken
k-mer
python
updated 12 months ago by
Ram
43k • written 7.0 years ago by
Sej Modha
5.3k
412 results • Page
3 of 9
Recent Votes
constructing pangenome through psvcp
Differential Expression with limma: Contrast and Design Matrix, combinatorial approach valid?
Differential Expression with limma: Contrast and Design Matrix, combinatorial approach valid?
Answer: RNAseq coverage vs depth for transcript isoform expression?
Answer: ChatGPT optimized for bioinformatics questions
Comment: ChatGPT optimized for bioinformatics questions
C: How can I perform Differential expression analysis with just one control and one
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Comment: constructing pangenome through psvcp
by
analyst
▴ 50
Fixed the issue by updating nucmer version.
Comment: Blastn error : ncbi::CObject::ThrowNullPointerException() - Attempt to access NU
by
GenoMax
142k
Can you create a small test database (`makeblastdb`) from your query file and try to run the search against the same file and see if that w…
Comment: calculating genomic coverage/ base overlap in R
by
1769mkc
★ 1.2k
you can `dput(head(df)` for the both the data frame so that other can test for possible solutions
Comment: Broad and Narrow peaks
by
ATpoint
82k
What is your question? It's unclear.
Comment: Help with Biopython for Beginner
by
Joe
21k
One question before offering more solutions: are you trying to learn Python with this as an example problem, or are you trying to find the …
Answer: RNAseq coverage vs depth for transcript isoform expression?
by
Gordon Smyth
★ 7.2k
See the exploration of isoform precision vs read length and sequencing depth in our paper: https://doi.org/10.1093/nar/gkad1167. Table 1 o…
Comment: How to handle duplicated genes in TCGA data?
by
txema.heredia
▴ 130
Why does the tool require gene symbols and not ensembl ids? Is it retrieving information from somewhere else? If so, your best bet is to fi…
Comment: how to treat the replicates while performing WGCNA
by
mavy
▴ 10
Thank you so much for your response . Really appreciate it. I will try the way you mentioned and will get back if I have any query
Comment: Blastn error : ncbi::CObject::ThrowNullPointerException() - Attempt to access NU
by
hophuquy0944
• 0
i have the same error, i used high performance computer, here is my code to set memory. srun --nodes=1 --ntasks=1 --cpus-per-task=24 -…
Comment: Overlapping Ranges within Granges object
by
Alex Reynolds
35k
Yes, `bedmap` will perform operations on one or two BED files.
Comment: B allele frequency (BAF)
by
aidangcruickshank
▴ 10
Apologies for resurrecting this post, but any idea what that functions "regions" paramater takes? Would it be a GRanges object? The documen…
Comment: How to handle duplicated genes in TCGA data?
by
Ngrin
• 0
Thanks @txema.heredia.The tool I am going to use only accepts gene symbols. This is the reason. So I cannot use ENS IDs.
Answer: Design for complex RNA-Seq experiment using Deseq2
by
swbarnes2
14k
This is a rather small experiment, I don't know that you can establish a meaningful baseline for each patient with a single pre sample, and…
Comment: GG Sankey plot
by
LauferVA
4.2k
@bk11 i changed this comment to an answer. if you disagree please let me know. thanks for sharing your knowledge. VAL
Comment: ComplexHeatmap - How to change fontsize of rowAnnotation
by
hannes.bongartz
• 0
Thanks for the input. Unfortunately, that didn't help either. I appreciate any other tips. Thank you
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