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353 results • Page
1 of 8
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1
vote
0
replies
156
views
Tutorial:
Analysis of Smart-Seq3 data with kallisto-bustools
single-cell
kallisto
transcriptomics
smart-seq3
pipeline
7 days ago by
firestar
★ 1.5k
10
votes
7
replies
759
views
Tutorial:
Sequence Alignment from Scratch with BWA
alignment
bwa
DNA
5 days ago by
barslmn
★ 1.2k
1
vote
1
reply
253
views
Tutorial:
Converting TSV file to VCF
vcf
preprocessing
frequency
updated 19 days ago by
Pierre Lindenbaum
152k • written 19 days ago by
barslmn
★ 1.2k
1
vote
0
replies
218
views
Tutorial:
Prediction of Ribosomal RNA Genes Using RNAmmer Software
rRNA
RNAmmer
Annotation
Genome
27 days ago by
Dr.Animo
▴ 40
0
votes
0
replies
312
views
Tutorial:
GEO data mining (III) - Gene pathway enrichment analysis with complete code sharing
geo
mining
enrichment
data
Gene
pathway
RNA-Seq
R
4 weeks ago by
Novogene
▴ 210
0
votes
0
replies
413
views
Tutorial:
GEO Data Mining (II) - Differential gene expression analysis and visualization with complete code sharing
geo
mining
differential
data
expression
RNA-Seq
gene
R
4 weeks ago by
Novogene
▴ 210
1
vote
0
replies
237
views
Tutorial:
GEO data mining (IB) - Downloading Sequence Read Archive (SRA) raw data
geo
mining
datasets
data
SRA
RNA-Seq
4 weeks ago by
Novogene
▴ 210
1
vote
0
replies
319
views
Tutorial:
Gene Expression Omnibus Data Mining (IA): Quick and easy download of GEO data
geo
mining
data
RNA-Seq
R
5 weeks ago by
Novogene
▴ 210
41
votes
1
reply
5.8k
views
Tutorial:
Basic normalization, batch correction and visualization of RNA-seq data
edger
tutorial
rna-seq
6 weeks ago by
ATpoint
68k
1
vote
3
replies
347
views
Tutorial:
Gibbs Sampling Algorithm Implementation for Searching DNA Motifs
montecarlo
DNA
motif
gibbs
sampling
splice
updated 6 weeks ago by
GenoMax
125k • written 6 weeks ago by
barslmn
★ 1.2k
76
votes
19
replies
68k
views
13 follow
Tutorial:
How to Install SamTools, HTSLib, and BCFTools on Ubuntu 18.04
samtools
bcftools
htslib
Tutorial
updated 8 days ago by
jcurry01
• 0 • written 4.5 years ago by
otwtgin2010
▴ 520
72
votes
60
replies
22k
views
16 follow
Tutorial:
Produce PCA bi-plot for 1000 Genomes Phase III in VCF format (old)
1000 genomes
PCA
VCF
PLINK
Tutorial
updated 8 weeks ago by
Mahmoud.Bassyouni
• 0 • written 5.4 years ago by
Kevin Blighe
84k
82
votes
28
replies
27k
views
19 follow
Tutorial:
How to create a mutation landscape (waterfall) plot with GenVisR
GenVisR
BioConductor
R
Graphics
Tutorial
updated 12 weeks ago by
GenoMax
125k • written 6.9 years ago by
Obi Griffith
20k
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
1
vote
2
replies
394
views
Tutorial:
ViennaRNA package installation in Windows
install
mfold
viennarna
rna
windows
updated 4 months ago by
Asaf
9.5k • written 4 months ago by
Sandhiya
▴ 20
1
vote
0
replies
242
views
Tutorial:
Making LDA Score plot
LDA
metagenomics
4 months ago by
rohitsatyam102
▴ 690
128
votes
122
replies
27k
views
23 follow
Tutorial:
Survival analysis with gene expression
survival analysis
cox
geo
gene expression
Tutorial
updated 4 months ago by
Athanasios
• 0 • written 4.3 years ago by
Kevin Blighe
84k
9
votes
7
replies
5.0k
views
Tutorial:
ClusterProfiler A software for functional enrichment of differentially expressed genes- A tutorial
Software
clusterProfiler
Tool
rna-seq
tool
updated 4 months ago by
Shubham
• 0 • written 23 months ago by
Novogene
▴ 210
11
votes
1
reply
2.0k
views
Tutorial:
Dealing with nanopore fast5 files compressed with vbz
hdf5
nanopore
fast5
vbz
MinKNOW
updated 5 months ago by
Assa Yeroslaviz
★ 1.8k • written 12 months ago by
dariober
14k
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
79
votes
21
replies
13k
views
16 follow
Tutorial:
Gene Set Enrichment Analysis
microarray
enrichment
Tutorial
GSEA
RNA-Seq
6 weeks ago by
Hamid Ghaedi
2.8k
3
votes
0
replies
406
views
Tutorial:
Automated dbSNP lookup by rsID position, plus genome build liftover
rsid
hg19
liftover
hg38
dbsnp
5 months ago by
Kevin Blighe
84k
27
votes
0
replies
2.5k
views
Tutorial:
Building Docker images
singularity
docker
container
6 months ago by
ATpoint
68k
1
vote
1
reply
12k
views
Tutorial:
Docker denied: requested access to the resource is denied
docker
updated 6 months ago by
Vincent Laufer
★ 2.5k • written 6 months ago by
kodwings
▴ 10
83
votes
34
replies
15k
views
21 follow
Tutorial:
Enrichment Analysis, Clustering and Scoring with pathfindR
R
pathway
enrichment
active subnetwork
Tutorial
updated 6 months ago by
Ram
37k • written 4.6 years ago by
egeulgen
★ 1.3k
78
votes
2
replies
53k
views
Tutorial:
How To Ask Good Questions On Technical And Scientific Forums
tutorial
Tutorial
written 9.6 years ago by
Eric Normandeau
11k
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
1
vote
1
reply
1.1k
views
Tutorial:
Generating count matrix for STAR counts in GDC v32.0 for RNA-Seq
TCGA
Counts
v32.0
Biolinks
GDC
STAR
updated 7 weeks ago by
bioinfonewbie
• 0 • written 9 months ago by
dare_devil
★ 1.7k
37
votes
8
replies
8.6k
views
10 follow
Tutorial:
Methylation Analysis Tutorial in R_part1
cancer
Tutorial
R
methylation
updated 8 weeks ago by
krushnach80
★ 1.1k • written 2.3 years ago by
Hamid Ghaedi
2.8k
3
votes
2
replies
1.1k
views
Tutorial:
Running fastq_screen on your data
fastqscreen
10 months ago by
rohitsatyam102
▴ 690
7
votes
14
replies
1.8k
views
6 follow
Tutorial:
Install required dependencies for GATK4 on remote server without root privilege
gatk
updated 3 months ago by
Angelina_G
• 0 • written 11 months ago by
thehung92phuyen
▴ 30
74
votes
14
replies
13k
views
15 follow
Tutorial:
List Of Bioinformatics Books
bioinformatics
tutorial
books
Tutorial
updated 4 months ago by
Ram
37k • written 9.7 years ago by
Medhat
9.5k
24
votes
13
replies
5.7k
views
9 follow
Tutorial:
How to get FASTQ reads from the Short Read Archive (SRA)
fastq
sra
updated 12 months ago by
liorglic
★ 1.1k • written 15 months ago by
Istvan Albert
96k
3
votes
13
replies
8.8k
views
Tutorial:
Merging multiple vcf files into Single vcf file
vcf
merge
bcftools
Tutorial
written 4.0 years ago by
jaybee
▴ 140
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
2
votes
0
replies
900
views
Tutorial:
Free Book : Computational Biology of a cell signalling pathway using R
cell
Biology
R
Computational
signalling
13 months ago by
sinha.shriprakash
▴ 20
0
votes
0
replies
7.7k
views
Tutorial:
Using PatMatch to search for nucleic and protein sequence patterns and integrate the results with Python/Jupyter for downstream analysis
Jupyter
Python
pattern
12 months ago by
Wayne
★ 1.5k
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
24
votes
10
replies
55k
views
9 follow
Tutorial:
Installing an updated R version (>=4.0) using conda
Tutorial
error
software
R
updated 8 months ago by
Chih
• 0 • written 22 months ago by
Nitin Narwade
★ 1.3k
6
votes
2
replies
2.1k
views
Tutorial:
Unsupervised clustering on gene expression data
gene
RNA-seq
expression
clustering
4 months ago by
Hamid Ghaedi
2.8k
41
votes
6
replies
17k
views
Tutorial:
Greatly speed up conda by using mamba
software
updated 12 months ago by
cameron.cowan
▴ 40 • written 22 months ago by
rpolicastro
10k
142
votes
68
replies
42k
views
18 follow
Tutorial:
Network plot from expression data in R using igraph
R
Tutorial
microarray
RNA-Seq
network
updated 7 months ago by
Guido
• 0 • written 5.2 years ago by
Kevin Blighe
84k
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
194
votes
44
replies
67k
views
33 follow
Tutorial:
Analysing Microarray Data In Bioconductor
microarray-analysis
bioconductor
updated 22 days ago by
Ram
37k • written 10.3 years ago by
Obi Griffith
20k
6
votes
2
replies
963
views
Tutorial:
GSE28955 - Agilent-016436 Human miRNA Microarray 1.0
limma
GPL6955
Microarray
miRNA
Agilent
17 months ago by
Kevin Blighe
84k
0
votes
0
replies
838
views
Tutorial:
Alignment-free RNA-seq Differential Gene Expression Analysis with Kallisto & Sleuth
dge
kallisto
rnaseq
sleuth
17 months ago by
mo
• 0
2
votes
0
replies
1.5k
views
Tutorial:
Affymetrix HTA 2.0 id conversion
biomart
HTA
affymetrix
Affymetrix
2.0
18 months ago by
Kevin Blighe
84k
45
votes
2
replies
35k
views
Tutorial:
Mapping Reads With Bwa And Bowtie
bowtie
bwa
tutorial
Tutorial
updated 18 months ago by
kjh98
• 0 • written 10.8 years ago by
MSU course 2011
▴ 540
92
votes
105
replies
32k
views
25 follow
Tutorial:
Produce PCA bi-plot for 1000 Genomes Phase III - Version 2
Tutorial
1000
genomes
PCA
PLINK
updated 11 hours ago by
s.w.vanderlaan
▴ 40 • written 4.4 years ago by
Kevin Blighe
84k
0
votes
0
replies
699
views
Tutorial:
Event & tutorial: open software tools and AI for improving bioimaging (SLURM, containerisation)
containerisation
bioimaging
SLURM
health
19 months ago by
Erin Haskell | ELIXIR
▴ 470
353 results • Page
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Recent Votes
A: Coursera Genomic Data Science courses
Coursera Genomic Data Science courses
The Biostar Herald for Monday, January 30, 2023
A: Python Cigar String - Finding Indels Break Points Positions
Comment: Strand-specific in HT-Seq
Comment: Calculating PRS in a large cohort
C: BWA MEM vs BOWTIE2 , which is best?
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Answer: How to change every third line in a fastq library
by
Ram
37k
`sed` can do this: sed '3~4s/.+/+/' in.fastq > out.fastq #untested, test on the first ~40 lines before running on entire file
Answer: Protein protein interactions
by
Mensur Dlakic
★ 22k
What you want to do can be be done only on a case-by-case basis, as there is no database that contains information about interacting residu…
Comment: Strand-specific in HT-Seq
by
ibq.enriquepola
• 0
thanks so much, I will try this tool.
Comment: Python Dictionary of Primer3-py Primer Designs
by
bhumm
▴ 10
@barslmn, thank you so much! This was exactly what I was looking for! For completeness (and for anyone else who may stumble across this po…
Comment: Calculating PRS in a large cohort
by
haasroni
• 0
Thank you! Do you know if possible to give a score file (--score) that has chr and positions instead of SNP IDs?
Comment: Strand-specific in HT-Seq
by
barrypraveen
▴ 100
Depends on the library preparation, if your cDNA is reverse complement then it should be -s <reverse>.
Comment: Is there a method to group and summarize the `homer` `findMotifsGenome.pl` outpu
by
ATpoint
68k
Can you give an example of how the output should look like?
Answer: Is there a method to group and summarize the `homer` `findMotifsGenome.pl` outpu
by
Mensur Dlakic
★ 22k
Don't know if there is a specific tool for this, but using your eyes should be sufficient to match similar sequence logos. For example, `B…
Comment: Strand-specific in HT-Seq
by
GenoMax
125k
There are multiple threads about this issue on biostars but here is a tool that can be used without alignments: https://www.biostars.org/p/…
Comment: translate CDS to prot formatted with nt nubers
by
vvasta
• 0
this is the format I am lookinf for ![enter image description here][1] [1]: /media/images/1d846c49-5646-4cf6-8a55-2897c1cd
Answer: POSSUM Bioinformatics Tool
by
Mensur Dlakic
★ 22k
The link to all UniRef databases: https://ftp.uniprot.org/pub/databases/uniprot/uniref/ When you select `uniref100`, the file you wan…
Comment: Where can I get the ICB datasets in this website?
by
GenoMax
125k
What is ICB therapies for those of us that do not know. The site you linked says `isb` something so is that the same as what you are lookin…
Answer: De novo motif in DNA sequences
by
Buffo
★ 2.0k
The [MEME][1] Suite can be a good start for you. [1]: https://meme-suite.org/meme/
Comment: How to Calulate Allele Frequency from a VCF File?
by
Jeremy Leipzig
21k
Hmm i would expect some heteroplasmy to show up in AD or DP at some positions
Answer: KMP algorithm's time complexity
by
umang
• 0
Not sure if this is the right forum to ask about KMP. Anyways you can read https://www.w3spot.com/2020/07/kmp-algorithm-explained-in-plain-…
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