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319 results • Page
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238
votes
176
replies
91k
views
73 follow
Tutorial:
Survival analysis of TCGA patients integrating gene expression (RNASeq) data
RNA-Seq
Survival
TCGA
updated 6 months ago by
Ram
41k • written 8.4 years ago by
TriS
★ 4.7k
132
votes
123
replies
35k
views
23 follow
Tutorial:
Survival analysis with gene expression
cox
gene-expression
survival-analysis
geo
updated 8 months ago by
1769mkc
★ 1.1k • written 5.1 years ago by
Kevin Blighe
86k
95
votes
105
replies
41k
views
25 follow
Tutorial:
Produce PCA bi-plot for 1000 Genomes Phase III - Version 2
1000genomes
PLINK
PCA
updated 9 months ago by
Ram
41k • written 5.3 years ago by
Kevin Blighe
86k
148
votes
70
replies
48k
views
20 follow
Tutorial:
Network plot from expression data in R using igraph
microarray
RNA-Seq
R
network
updated 3 months ago by
Raheleh
▴ 260 • written 6.1 years ago by
Kevin Blighe
86k
76
votes
70
replies
18k
views
18 follow
Tutorial:
Clustering of DAVID gene enrichment results from gene expression studies
enrichment
david
updated 9 months ago by
Ram
41k • written 5.8 years ago by
Kevin Blighe
86k
117
votes
66
replies
44k
views
20 follow
Tutorial:
[Deprecated] Fast download of FASTQ files from the European Nucleotide Archive (ENA)
aspera
fastq-dump
Fastq
ENA
updated 9 months ago by
Ram
41k • written 5.4 years ago by
ATpoint
78k
73
votes
60
replies
26k
views
16 follow
Tutorial:
Produce PCA bi-plot for 1000 Genomes Phase III in VCF format (old)
1000genomes
PLINK
PCA
VCF
updated 10 months ago by
Ram
41k • written 6.3 years ago by
Kevin Blighe
86k
60
votes
52
replies
42k
views
23 follow
Tutorial:
Creating Interactive Volcano Plots with R and Plot.ly
plotly
R
volcano-plot
updated 9 months ago by
Ram
41k • written 7.2 years ago by
steve
★ 3.4k
72
votes
48
replies
17k
views
15 follow
Tutorial:
For Short Reads, Which Aligners Find All Hits Given Certain Edit Distance Threshold?
ngs
alignment
bwa
updated 9 months ago by
Ram
41k • written 10.8 years ago by
lh3
33k
90
votes
48
replies
31k
views
29 follow
Tutorial:
Extract Total Non-Overlapping Exon Length Per Gene With Bioconductor
fpkm
rna-seq
bioconductor
updated 5 weeks ago by
Ram
41k • written 10.2 years ago by
Irsan
★ 7.8k
196
votes
44
replies
70k
views
33 follow
Tutorial:
Analysing Microarray Data In Bioconductor
microarray-analysis
bioconductor
updated 11 months ago by
Ram
41k • written 11.2 years ago by
Obi Griffith
20k
59
votes
43
replies
20k
views
18 follow
Tutorial:
Polish PacBio assembly with latest PacBio tools : an affordable solution for everyone
pbalign
pacbio
arrow
smrt-limk
updated 9 months ago by
Ram
41k • written 6.2 years ago by
Rox
★ 1.4k
282
votes
39
replies
177k
views
29 follow
Tutorial:
How to download raw sequence data from GEO/SRA
fastq
SRA
bam
GEO
updated 8 months ago by
Ram
41k • written 9.3 years ago by
Obi Griffith
20k
149
votes
35
replies
61k
views
33 follow
Tutorial:
Tools For Metagenomic Data Analysis
metagenomics
next-gen
updated 9 months ago by
Ram
41k • written 11.0 years ago by
vijay
★ 1.6k
147
votes
34
replies
53k
views
17 follow
Tutorial:
Working with MAF files (Mutation Annotation Format) from the TCGA (The Cancer Genome Atlas)
music
cancer
tcga
mutation
maf
updated 9 months ago by
Ram
41k • written 10.7 years ago by
Cyriac Kandoth
6.0k
83
votes
34
replies
17k
views
22 follow
Tutorial:
Enrichment Analysis, Clustering and Scoring with pathfindR
enrichment
R
pathway
active-subnetwork
updated 6 months ago by
adelheidkratzer
• 0 • written 5.5 years ago by
egeulgen
★ 1.3k
290
votes
33
replies
102k
views
25 follow
Tutorial:
Cheat Sheet For One-Based Vs Zero-Based Coordinate Systems
coordinates
updated 9 months ago by
Ram
41k • written 10.1 years ago by
Obi Griffith
20k
10
votes
31
replies
10.0k
views
10 follow
Tutorial:
OrthoMCL installation on Ubuntu Linux
ubuntu
orthomcl
mysql
linux
updated 6 weeks ago by
ha2606
• 0 • written 5.9 years ago by
vimalkvn
▴ 320
14
votes
31
replies
6.1k
views
6 follow
Tutorial:
gene set filter/selection for training ab initio annotation tools
geneset
genome
gene
abinitio
updated 9 months ago by
Ram
41k • written 4.3 years ago by
Juke34
8.4k
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
ATpoint
78k • written 7.8 years ago by
Ram
41k
84
votes
29
replies
30k
views
20 follow
Tutorial:
How to create a mutation landscape (waterfall) plot with GenVisR
BioConductor
GenVisR
Graphics
R
updated 4 months ago by
amziepickles
• 0 • written 7.8 years ago by
Obi Griffith
20k
72
votes
27
replies
27k
views
16 follow
Tutorial:
How To Separate Illumina Based Strand Specific Rna-Seq Alignments By Strand
RNA-seq
updated 7 days ago by
snardeli
• 0 • written 9.8 years ago by
Istvan Albert
99k
64
votes
26
replies
13k
views
7 follow
Tutorial:
Parallel processing in R
biocparallel
mclapply
foreach
R
updated 9 months ago by
Ram
41k • written 6.2 years ago by
Kevin Blighe
86k
65
votes
26
replies
13k
views
11 follow
Tutorial:
Generating consensus sequence from bam file
fasta
consensus
bam
updated 9 months ago by
Ram
41k • written 4.8 years ago by
finswimmer
16k
58
votes
25
replies
39k
views
15 follow
Tutorial:
Protocol To Downlad TCGA Data From GDC
GDC
methylation
TCGA
updated 8 months ago by
Ram
41k • written 7.4 years ago by
Shicheng Guo
★ 9.3k
95
votes
25
replies
32k
views
11 follow
Tutorial:
Fastq Quality Control Shootout
quality
qc
trimming
fastq
updated 9 months ago by
Ram
41k • written 11.2 years ago by
Istvan Albert
99k
18
votes
22
replies
8.5k
views
10 follow
Tutorial:
Create de novo repeat library
de-novo
repeat
annotation
updated 11 weeks ago by
evoecogen
▴ 20 • written 4.0 years ago by
Juke34
8.4k
88
votes
22
replies
84k
views
14 follow
Tutorial:
How to Install SamTools, HTSLib, and BCFTools on Ubuntu 18.04
bcftools
samtools
htslib
updated 5 months ago by
sifa.khan
• 0 • written 5.4 years ago by
otwtgin2010
▴ 580
84
votes
21
replies
20k
views
16 follow
Tutorial:
Gene Set Enrichment Analysis
microarray
enrichment
RNA-Seq
GSEA
updated 9 months ago by
Ram
41k • written 3.2 years ago by
Hamid Ghaedi
3.1k
12
votes
20
replies
13k
views
10 follow
Tutorial:
Associating VDJ clonotyping data with scRNA-seq in Seurat
single-cell
RNA-Seq
seurat
TCR
updated 9 months ago by
Ram
41k • written 4.5 years ago by
jared.andrews07
★ 16k
53
votes
19
replies
43k
views
6 follow
Tutorial:
Visualizing Chip-Seq Data Using Ucsc [Bigwig]
visualization
bigwig
chip-seq
rna-seq
updated 9 months ago by
Ram
41k • written 11.7 years ago by
Sukhi Singh
11k
8
votes
19
replies
13k
views
9 follow
Tutorial:
A:orthomcl with local mysql server on linux server, complete install
mysql
orthomcl
updated 9 months ago by
Ram
41k • written 9.1 years ago by
Lesley Sitter
▴ 600
90
votes
19
replies
31k
views
12 follow
Tutorial:
Machine Learning For Cancer Classification - Part 1 - Preparing The Data Sets
microarray
bioconductor
expression
classification
updated 9 months ago by
Ram
41k • written 10.1 years ago by
Obi Griffith
20k
42
votes
19
replies
7.6k
views
8 follow
Tutorial:
Designing Command-Line Interfaces (Clis) For Scientific Software
software
updated 9 months ago by
Ram
41k • written 10.8 years ago by
Daniel Standage
4.1k
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
Ram
41k • written 7.2 years ago by
chen
★ 2.5k
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
Ram
41k • written 10.8 years ago by
Istvan Albert
99k
12
votes
17
replies
2.7k
views
Tutorial:
How to find the mapping percentages for data deposited in the Zaire ebolavirus bioproject from the 2014 outbreak
ebola
bwa
updated 11 months ago by
Ram
41k • written 8.5 years ago by
Istvan Albert
99k
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
GenoMax
136k • written 10.1 years ago by
Obi Griffith
20k
99
votes
16
replies
32k
views
18 follow
Tutorial:
Heatmaps in R
heatmap
R
updated 9 months ago by
Ram
41k • written 7.4 years ago by
Jean-Karim Heriche
26k
63
votes
15
replies
13k
views
Tutorial:
Which human reference genome should I use?
assembly
genome
alignment
updated 6 months ago by
Ram
41k • written 5.2 years ago by
finswimmer
16k
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
Ram
41k • written 10.9 years ago by
Medhat
9.7k
34
votes
15
replies
19k
views
12 follow
Tutorial:
TCGA UUIDS to TCGA barcode (SampleID) in R
next-gen
GDC
R
TCGA
updated 9 months ago by
Ram
41k • written 7.2 years ago by
martinguerrerog89
▴ 310
34
votes
15
replies
6.0k
views
6 follow
Tutorial:
How to do data cleaning for VCF genetic file
vcf
updated 9 months ago by
Ram
41k • written 4.5 years ago by
Shicheng Guo
★ 9.3k
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
Ram
41k • written 10.9 years ago by
Cyriac Kandoth
6.0k
51
votes
14
replies
80k
views
10 follow
Tutorial:
Using R in Conda
R
updated 9 months ago by
Ram
41k • written 3.4 years ago by
rohitsatyam102
▴ 780
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
Ram
41k • written 7.6 years ago by
Mads Lerdrup
▴ 460
36
votes
14
replies
32k
views
14 follow
Tutorial:
installing samtools with conda - overcoming two common errors
samtools
conda
updated 4 weeks ago by
psschlogl
▴ 50 • written 3.3 years ago by
lavinia.gordon
▴ 160
75
votes
14
replies
15k
views
15 follow
Tutorial:
List Of Bioinformatics Books
books
updated 10 months ago by
Ram
41k • written 10.6 years ago by
Medhat
9.7k
4
votes
13
replies
12k
views
Tutorial:
Merging multiple vcf files into Single vcf file
vcf
bcftools
updated 5 months ago by
Ram
41k • written 4.8 years ago by
jaybee
▴ 140
19
votes
13
replies
8.1k
views
10 follow
Tutorial:
Setting up Aspera Connect (ascp) on Linux and macOS
ascp
aspera
updated 5 weeks ago by
jude
• 0 • written 17 months ago by
ATpoint
78k
319 results • Page
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Recent Votes
The Biostar Herald for Monday, December 11, 2023
Comment: GATK GetPileupSummaries Java heap space
The Biostar Herald for Monday, December 11, 2023
A: How To Sort Sam File
Answer: GATK GetPileupSummaries Java heap space
Answer: Autocompleting paths within scripts
Are Variable Features ranked in seurat?
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Comment: How should I run ssgsea analysis ?
by
Ram
41k
Just add a statement to your comments stating that the text was generated using ChatGPT - it is a good tool but it's not aware of its own s…
Comment: Autocompleting paths within scripts
by
DanielEB_fisk
▴ 20
Yep, sorry, you are right it is not a bioinformatics question. I asked here because it relates with the work we do anyway.
Comment: autodock vina on mac
by
Ram
41k
That section is for after you have virtualbox set up. You may have to run a really old version of macOS within the virtualbox, so be prepar…
Comment: ChatGPT optimized for bioinformatics questions
by
Ram
41k
I understand. The purpose of my comment is to serve as feedback.
Comment: How can I obtain the DNA sequences of each CDS for several genbank files?
by
Ram
41k
Look into passing command line parameters to a python script. You can pass the input file name as a parameter to the script and execute the…
Answer: Autocompleting paths within scripts
by
Michael
53k
Not really a Bioinformatics question but generally very useful: [vim can do that][1] [type some prefix of path]<Ctrl-x><Ctrl-f> This…
Comment: How can I obtain the DNA sequences of each CDS for several genbank files?
by
Raphaëlle
• 0
Hello, Thank you very much for your quick reply. That was indeed the issue! Another question: is there a simple way of automating this …
Answer: Cluster sub-set analysis using Seurat
by
j.gleixner
▴ 10
There now is also `Seurat::FindSubCluster`
Comment: How can i control the cluster number in scRNASeq clustering by Seurat package
by
j.gleixner
▴ 10
There is now also Seurat::BuildClusterTree that makes this easier.
Answer: How can i control the cluster number in scRNASeq clustering by Seurat package
by
j.gleixner
▴ 10
If you want to get a certain number of clusters without resorting to trying different settings for the resolution parameter, you can firs…
Answer: How to speed-up to contruct phylogenetic tree
by
Nelo
▴ 20
I will also try this `fasttree`
Comment: i ues schicexplorer's hicbuildmatrix code complains that two sam files do not ha
by
1125195245
• 0
I tried using bowtie2's --reorder command to output a sam file for each of the two files, and then used both sam files to build the matrix,…
Comment: How to speed-up to contruct phylogenetic tree
by
Nelo
▴ 20
I used MEGA CC (comand line option) but there is no option to specify threads in its `--help` manual . And default thread is 4
Comment: How to speed-up to contruct phylogenetic tree
by
Nelo
▴ 20
The average length of fasta sequences is ~300aa length. I can't exclude any sequences as I have to provide them nomenclature aslo on the ba…
Comment: How to speed-up to contruct phylogenetic tree
by
Nelo
▴ 20
I used Raxml for a trial fasta file of about only 33 sequences as: `raxmlHPC-PTHREADS-AVX -f a -T 80 -m PROTGAMMAWAG -n test1 -s bittergou…
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