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353 results • Page
3 of 8
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19
votes
9
replies
6.0k
views
8 follow
Tutorial:
Interactive Perl Learning
Tutorial
perl
tutorial
updated 16 months ago by
Ram
37k • written 9.6 years ago by
Medhat
9.5k
18
votes
2
replies
9.5k
views
Tutorial:
Video: RNA-Seq Alignment and Visualization using Galaxy and IGB
RNA-Seq
Galaxy
IGB
updated 10 months ago by
Ram
37k • written 8.3 years ago by
Nowlan Freese
▴ 860
18
votes
2
replies
5.4k
views
Tutorial:
Update kraken databases
kraken
k-mer
database
python
Tutorial
4.9 years ago by
Sej Modha
5.2k
18
votes
21
replies
6.6k
views
10 follow
Tutorial:
Create de novo repeat library
de-novo
repeat
Tutorial
annotation
updated 6 weeks ago by
evoecogen
▴ 20 • written 3.2 years ago by
Juke34
7.5k
17
votes
40
replies
15k
views
16 follow
Tutorial:
Easy way to run easily orthoMCL (Copy & paste)
run
easy
orthomcl
all-v-all
mcl
Tutorial
updated 2.2 years ago by
Buffo
★ 2.0k • written 6.6 years ago by
Esaie
▴ 160
17
votes
3
replies
11k
views
Tutorial:
bedGraphToBigWig Tutorial and Report
bedGraphToBigWig
updated 6 months ago by
Ram
37k • written 7.0 years ago by
Shicheng Guo
★ 9.2k
17
votes
9
replies
4.2k
views
Tutorial:
Finding the significance of the overlap between 2 or more gene sets using simulation in R.
R
tidyverse
gene
Tutorial
updated 16 months ago by
krushnach80
★ 1.1k • written 2.4 years ago by
rpolicastro
10k
17
votes
13
replies
1.6k
views
Tutorial:
Screen shots of text (please don't)!
meta
Forum
Tutorial
5.8 years ago by
Michael Dondrup
52k
16
votes
11
replies
7.2k
views
Tutorial:
How to Use Biostars, Part II: Post types, Deleting, (Un)Subscribing, Linking and Bookmarking
meta
how-to
documentation
Tutorial
5 months ago by
Ram
37k
16
votes
5
replies
8.3k
views
Tutorial:
Using The Biomart Perl Api For Simple Queries
biomart
perl
api
tutorial
Tutorial
updated 4 months ago by
Ram
37k • written 10.4 years ago by
Obi Griffith
20k
16
votes
0
replies
12k
views
Tutorial:
Workshop - Analysis Of Next Generation Sequencing Data
rna-seq
analysis
tutorial
Tutorial
updated 10.5 years ago by
Leonor Palmeira
3.8k • written 10.8 years ago by
David Langenberger
9.8k
16
votes
7
replies
12k
views
Tutorial:
Integrating VDJ sequencing data with Seurat
Seurat
clonotyping
VDJ
sc-RNAseq
Tutorial
updated 23 months ago by
Friederike
8.6k • written 3.6 years ago by
atakanekiz
▴ 310
16
votes
11
replies
13k
views
7 follow
Tutorial:
retrieve full TCGA datasets from cBioportal with R
cBioportal
TCGA
data_retrieval
RNASeq
R
Tutorial
updated 3.7 years ago by
raffael.azevedo
▴ 30 • written 6.3 years ago by
TriS
★ 4.6k
15
votes
1
reply
6.0k
views
Tutorial:
A compilation of conversion tools for BED, SAM/BAM, psl, pslx, blast tabular and blast xml
BED
SAM
psl
blast
Tutorial
5.2 years ago by
Joseph Hughes
★ 3.0k
15
votes
5
replies
11k
views
6 follow
Tutorial:
Easy way to do GO enrichment in R
enrichr
gene
RNA-Seq
R
Tutorial
updated 8 months ago by
Kevin Blighe
84k • written 5.2 years ago by
ahmad mousavi
▴ 740
15
votes
2
replies
6.4k
views
Tutorial:
Genotype And Snp Calling Review Papers
snp
tutorial
Tutorial
updated 6.0 years ago by
willgilks
▴ 350 • written 10.4 years ago by
Istvan Albert
96k
15
votes
5
replies
13k
views
Tutorial:
How to create a mutation lolliplot with GenVisR
genvisr
graphics
bioconductor
R
Tutorial
updated 6.4 years ago by
mia1260
• 0 • written 6.6 years ago by
Obi Griffith
20k
15
votes
2
replies
2.7k
views
Tutorial:
Introduction to bedtools.
bedtools
tutorial
Tutorial
updated 11 months ago by
Ram
37k • written 8.2 years ago by
Aaronquinlan
11k
15
votes
2
replies
1.3k
views
Tutorial:
Germline variant calling pipeline using Snakemake
snakemake
GATK
germline_variant_calling
updated 3 months ago by
brunobsouzaa
▴ 790 • written 16 months ago by
nhaus
▴ 270
15
votes
1
reply
2.9k
views
Tutorial:
Current Topics in Genome Analysis 2016 (collection of educational lectures)
workshop
training
genomics
lectures
Tutorial
6.7 years ago by
Malachi Griffith
19k
15
votes
3
replies
4.1k
views
Tutorial:
NCBI blast tutorial
ncbi
blast
tutorial
Tutorial
updated 6.8 years ago by
Jenez
▴ 540 • written 6.8 years ago by
Eric Normandeau
11k
15
votes
0
replies
6.3k
views
Tutorial:
Introduction To Ngs Bioinformatics By The Bioinformatics Team At The University Of Texas
bioinformatics
training
tutorial
Tutorial
10.6 years ago by
Istvan Albert
96k
14
votes
7
replies
5.4k
views
Tutorial:
Visualization of ChIP-Seq peak overlaps using HOMER mergePeaks and UpSetR
ChIP-Seq
R
HOMER
peaks
Tutorial
3.5 years ago by
steve
★ 3.3k
14
votes
2
replies
6.0k
views
Tutorial:
ChIP-seq analysis tutorial
Tutorials
ChIP-Seq
updated 4 months ago by
Ram
37k • written 7.4 years ago by
Ming Tang
★ 2.9k
14
votes
0
replies
8.7k
views
Tutorial:
How to generate PCA plot and heatmaps in R
RNA-Seq
R
PCA
heatmap
Tutorial
6.4 years ago by
Ming Tang
★ 2.9k
14
votes
0
replies
7.9k
views
Tutorial:
Video: ChIP-Seq Analysis and Visualization using Galaxy and IGB.
IGB
ChIP-Seq
Galaxy
MACS
RNA-Seq
updated 10 months ago by
Ram
37k • written 8.0 years ago by
Nowlan Freese
▴ 860
14
votes
2
replies
2.6k
views
Tutorial:
Methylation Analysis Tutorial in R_part2
RNA-Seq
R
methylation
Tutorial
cancer
4 months ago by
Hamid Ghaedi
2.8k
14
votes
2
replies
2.1k
views
Tutorial:
Exploring OpenSNP - an RMarkdown report on crowdsourced genotypes and phenotypes
SNP
R
Tutorial
5.0 years ago by
Jeremy Leipzig
21k
13
votes
6
replies
5.1k
views
Tutorial:
Trim & align paired-end reads in a single pass
trim
align
paired-end fastq
pipe
Tutorial
6.6 years ago by
dariober
14k
13
votes
9
replies
3.5k
views
Tutorial:
TCGA transcriptome data to R (DESeq2)
TCGA
GDC
DESeq2
updated 7 months ago by
dk0319
▴ 40 • written 14 months ago by
Barry Digby
★ 1.1k
13
votes
3
replies
4.6k
views
Tutorial:
Video: Visualization of whole genome DNA methylation data in IGB
Bismark
BS-Seq
RNA-Seq
IGB
updated 8 months ago by
Ram
37k • written 7.9 years ago by
Nowlan Freese
▴ 860
13
votes
8
replies
2.4k
views
Tutorial:
Setting up Aspera Connect (ascp) on Linux and macOS
aspera
ascp
10 weeks ago by
ATpoint
68k
13
votes
4
replies
4.0k
views
Tutorial:
RNASeq tutorial for gene differential expression analysis
R
RNA-Seq
Transcriptomics
Tutorial
bioconductor
12 months ago by
Thind amarinder
▴ 280
12
votes
6
replies
5.6k
views
Tutorial:
How to make your snakefiles self-documenting
snakemake
Tutorial
updated 5.9 years ago by
Eric Lim
★ 2.0k • written 6.2 years ago by
Botond Sipos
★ 1.7k
12
votes
31
replies
4.5k
views
6 follow
Tutorial:
gene set filter/selection for training ab initio annotation tools
gene
geneset
abinitio
Tutorial
genome
3 months ago by
Juke34
7.5k
12
votes
1
reply
4.7k
views
Tutorial:
scRNA-seq CITE-seq-count bioinformatics
RNA-Seq
CITE-seq-count
Tutorial
scRNA-seq
5 months ago by
colindaven
4.4k
12
votes
1
reply
1.8k
views
Tutorial:
PCR Primer or Primer+Probe design
pcr
probe
rt-pcr
qpcr
primer
updated 20 months ago by
jared.andrews07
★ 14k • written 20 months ago by
Kevin Blighe
84k
12
votes
0
replies
7.2k
views
Tutorial:
Plot average methylation levels across TSS region
bedtools
RRBS
R
methylation
updated 9 months ago by
Ram
37k • written 8.0 years ago by
TriS
★ 4.6k
12
votes
5
replies
7.5k
views
Tutorial:
How To Install BioPerl Without Root Privileges in Ubuntu/Linxu
bioperl
Tutorial
6.3 years ago by
Shicheng Guo
★ 9.2k
12
votes
11
replies
6.5k
views
Tutorial:
How to upload your RNA-Seq data to NCBI Sequence Read Archive (SRA)
NCBI
SRA
Bioproject
BioSample
Tutorial
updated 5.5 years ago by
Lucila
▴ 20 • written 5.9 years ago by
CandiceChuDVM
★ 2.4k
12
votes
4
replies
4.2k
views
Tutorial:
*FREE course* Bioinformatics for Biologists: An Introduction to Linux, Bash Scripting, and R
Tutorial
linux
bioinformatics
R
updated 14 months ago by
iamsmor
• 0 • written 24 months ago by
garden_giessen
▴ 120
12
votes
0
replies
2.0k
views
Tutorial:
Long versus wide data for plotting genomics data in R.
R
tidyverse
ggplot2
Tutorial
data.table
22 months ago by
rpolicastro
10k
12
votes
17
replies
2.2k
views
Tutorial:
How to find the mapping percentages for data deposited in the Zaire ebolavirus bioproject from the 2014 outbreak
ebola
bwa
updated 5 weeks ago by
Ram
37k • written 7.6 years ago by
Istvan Albert
96k
12
votes
4
replies
1.8k
views
Tutorial:
Tutorials for Library Normalization in DESeq2 and EdgeR
#DESeq2
#EdgeR
#normalization
Tutorial
5.4 years ago by
KVC_bioinfo
▴ 560
12
votes
1
reply
4.7k
views
Tutorial:
RepSeq data processing and analysis
immunology
tcr
repseq
sequencing
repertoire
updated 3 months ago by
Ram
37k • written 7.5 years ago by
mikhail.shugay
3.5k
12
votes
20
replies
11k
views
10 follow
Tutorial:
Associating VDJ clonotyping data with scRNA-seq in Seurat
seurat
single cell
RNA-Seq
TCR
Tutorial
20 months ago by
jared.andrews07
★ 14k
12
votes
2
replies
976
views
Tutorial:
Factors in R - How do they work, and how did I break my data?
R
Tutorial
22 months ago by
rpolicastro
10k
11
votes
1
reply
2.1k
views
Tutorial:
Guidelines for the computational analysis of single-cell RNA sequencing data
scRNA-seq
Tutorial
updated 14 months ago by
ATpoint
68k • written 2.1 years ago by
Mensur Dlakic
★ 22k
11
votes
6
replies
4.5k
views
Tutorial:
sharing some naive codes for microarray normalization in R with whom are too new in R alike me
R
updated 6 months ago by
Ram
37k • written 7.0 years ago by
fi1d18
★ 4.1k
11
votes
3
replies
1.1k
views
Tutorial:
Creating great documentation for bioinformatics software
Software Documentation
Tutorial
6.5 years ago by
venu
7.0k
353 results • Page
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Recent Votes
C: Reorder heatmap rows in a dataset with missing values
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Answer: Base recalibration in normal vs. tumor somatic variant calling in WXS data?
A: from .BAM to .BAI using samtools
Comment: bgzip error 4
Answer: Gene Set Enrichment Analysis, pathway, metabolism
Answer: Gene Set Enrichment Analysis, pathway, metabolism
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Recent Replies
Answer: trainGlimmerHMM Error while training a genome
by
congliu37
• 0
Hello, I got the same error using ~20,000 genes for training and it was solved by reducing training gene set. I assume GlimmerHMM was no…
Comment: How to Calulate Allele Frequency from a VCF File?
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Jeremy Leipzig
21k
That's correct. You don't have biallelic alleles in mitochondria, so you can use either the Allele depth (AD) or depth of coverage (DP) for…
Comment: How to calculate tumor mutation burden (TMB)?
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I just published a [post][1] on my blog, in which I include a simple R function for computing TMB. Try to see if that helps. I followed the…
Comment: Gene Set Enrichment Analysis, pathway, metabolism
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Thank you FrankStarling, ATpoint, jv, these were so helpful.
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vvasta
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I tried several of the online DNA translation tools but have not found one that would output DNA/prot alignment with nucleotide number w…
Comment: How possible deadlocks are there while migrating from MYISAM to InnoDb?
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but you already knew it. https://www.biostars.org/p/9551097/#9551098
Comment: How possible deadlocks are there while migrating from MYISAM to InnoDb?
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Pierre Lindenbaum
152k
your question is not related to bioinformatics. Ask stackoverflow.com.
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Hi lumos. It is not very clear to me what kind of information are you using for the test and how are you measuring cis-regulation. Are you …
Comment: Error 134 while aligning using hisat2
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Fabio Marroni
★ 2.9k
Other instances of the same error were indeed related to disk [space][1]. Can you post the output of the command: `df -h /bams/`? Another p…
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Pierre Lindenbaum
152k
``` Please ensure that your file is TAB delimited (e.g., cat -t FILE). - Also ensure that your file has integer chromosome coordinates in t…
Comment: bgzip error 4
by
Pierre Lindenbaum
152k
I/O error. Where are you writing , which filesytem ? do you have enough space ? what is the output of gzip < chr1.vcf.gz > chr1.vcf.gz…
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Neel
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**Error: unable to open file or unable to determine types for file** Hi i am trying to run this commands **bedtools intersect -a Ec_k1…
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Asan Emirsale
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You should find complementary sequences to make the miRNA silent. Should it be the Biopython or another tool. The solution might be as simp…
Comment: counting reads in a fastq file using a refrence fasta file
by
vaslanzadeh
▴ 10
Thanks, this works but it is extremely slow, is there any other alternatives?
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