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348 results • Page
1 of 7
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Views
Votes
Replies
233
votes
176
replies
78k
views
73 follow
Tutorial:
Survival analysis of TCGA patients integrating gene expression (RNASeq) data
RNA-Seq
TCGA
Survival
Tutorial
updated 3 months ago by
Ram
36k • written 6.9 years ago by
TriS
★ 4.5k
122
votes
119
replies
23k
views
22 follow
Tutorial:
Survival analysis with gene expression
survival analysis
cox
geo
gene expression
Tutorial
6 weeks ago by
Kevin Blighe
81k
86
votes
95
replies
28k
views
23 follow
Tutorial:
Produce PCA bi-plot for 1000 Genomes Phase III - Version 2
Tutorial
1000
genomes
PCA
PLINK
updated 6 weeks ago by
dongxinyu510
• 0 • written 3.8 years ago by
Kevin Blighe
81k
75
votes
70
replies
14k
views
18 follow
Tutorial:
Clustering of DAVID gene enrichment results from gene expression studies
enrichment
Tutorial
david
updated 5 months ago by
Kristy
• 0 • written 4.4 years ago by
Kevin Blighe
81k
139
votes
67
replies
38k
views
17 follow
Tutorial:
Network plot from expression data in R using igraph
R
Tutorial
microarray
RNA-Seq
network
updated 8 months ago by
Hamtaro
▴ 10 • written 4.6 years ago by
Kevin Blighe
81k
113
votes
66
replies
35k
views
20 follow
Tutorial:
[Deprecated] Fast download of FASTQ files from the European Nucleotide Archive (ENA)
aspera
fastq-dump
ENA
Fastq
Tutorial
11 months ago by
ATpoint
62k
72
votes
59
replies
20k
views
15 follow
Tutorial:
Produce PCA bi-plot for 1000 Genomes Phase III in VCF format (old)
1000 genomes
PCA
VCF
PLINK
Tutorial
updated 8 months ago by
sara27888
• 0 • written 4.8 years ago by
Kevin Blighe
81k
60
votes
49
replies
36k
views
22 follow
Tutorial:
Creating Interactive Volcano Plots with R and Plot.ly
R
plotly
volcano plot
Tutorial
updated 13 months ago by
Ram
36k • written 5.7 years ago by
steve
★ 3.2k
72
votes
48
replies
14k
views
15 follow
Tutorial:
For Short Reads, Which Aligners Find All Hits Given Certain Edit Distance Threshold?
bwa
alignment
ngs
tutorial
Tutorial
updated 11 weeks ago by
Ram
36k • written 9.4 years ago by
lh3
33k
192
votes
47
replies
66k
views
33 follow
Tutorial:
Analysing Microarray Data In Bioconductor
tutorial
bioconductor
microarray
analysis
tutorial
Tutorial
updated 4 months ago by
javanokendo
▴ 10 • written 9.7 years ago by
Obi Griffith
19k
55
votes
41
replies
17k
views
16 follow
Tutorial:
Polish PacBio assembly with latest PacBio tools : an affordable solution for everyone
arrow
pbalign
pacbio
polishing
smrt limk
Tutorial
updated 2.1 years ago by
zjl1983
• 0 • written 4.8 years ago by
Rox
★ 1.4k
75
votes
40
replies
25k
views
23 follow
Tutorial:
Extract Total Non-Overlapping Exon Length Per Gene With Bioconductor
fpkm
rna-seq
bioconductor
updated 3 months ago by
Ram
36k • written 8.7 years ago by
Irsan
★ 7.5k
17
votes
40
replies
14k
views
16 follow
Tutorial:
Easy way to run easily orthoMCL (Copy & paste)
run
easy
orthomcl
all-v-all
mcl
Tutorial
updated 19 months ago by
Buffo
★ 1.9k • written 6.0 years ago by
Esaie
▴ 160
269
votes
39
replies
150k
views
29 follow
Tutorial:
How to download raw sequence data from GEO/SRA
fastq
SRA
download
GEO
bam
updated 8 weeks ago by
Ram
36k • written 7.8 years ago by
Obi Griffith
19k
147
votes
35
replies
55k
views
33 follow
Tutorial:
Tools For Metagenomic Data Analysis
metagenomics
Tutorial
next-gen
updated 6 weeks ago by
Bramadi Arya
• 0 • written 9.6 years ago by
vijay
★ 1.6k
142
votes
34
replies
49k
views
17 follow
Tutorial:
Working with MAF files (Mutation Annotation Format) from the TCGA (The Cancer Genome Atlas)
mutation
maf
tcga
cancer
music
Tutorial
updated 6 weeks ago by
Ram
36k • written 9.2 years ago by
Cyriac Kandoth
5.8k
264
votes
33
replies
82k
views
24 follow
Tutorial:
Cheat Sheet For One-Based Vs Zero-Based Coordinate Systems
coordinates
tutorial
Tutorial
updated 4 months ago by
tshtatland
▴ 100 • written 8.7 years ago by
Obi Griffith
19k
41
votes
33
replies
6.1k
views
8 follow
Tutorial:
How to Use Biostars, Part-I: Questions, Answers, Comments and Replies
meta
how-to
documentation
Tutorial
19 months ago by
Ram
36k
76
votes
32
replies
13k
views
17 follow
Tutorial:
Enrichment Analysis, Clustering and Scoring with pathfindR
R
pathway
enrichment
active subnetwork
Tutorial
updated 16 months ago by
VolEr
▴ 30 • written 4.0 years ago by
egeulgen
★ 1.2k
81
votes
27
replies
25k
views
18 follow
Tutorial:
How to create a mutation landscape (waterfall) plot with GenVisR
GenVisR
BioConductor
R
Graphics
Tutorial
updated 6 months ago by
isd1989
• 0 • written 6.3 years ago by
Obi Griffith
19k
61
votes
26
replies
8.4k
views
11 follow
Tutorial:
Generating consensus sequence from bam file
bam
consensus
fasta
Tutorial
updated 13 months ago by
bioinfo8
▴ 180 • written 3.3 years ago by
finswimmer
15k
63
votes
26
replies
9.9k
views
7 follow
Tutorial:
Parallel processing in R
R
Tutorial
biocparallel
mclapply
foreach
2.6 years ago by
Kevin Blighe
81k
11
votes
26
replies
3.2k
views
Tutorial:
gene set filter/selection for training ab initio annotation tools
genome
gene
Tutorial
updated 11 months ago by
Picasa
▴ 610 • written 2.9 years ago by
Juke34
★ 7.1k
63
votes
25
replies
22k
views
14 follow
Tutorial:
How To Separate Illumina Based Strand Specific Rna-Seq Alignments By Strand
rna-seq
tutorial
Tutorial
updated 2.1 years ago by
Ram
36k • written 8.4 years ago by
Istvan Albert
93k
128
votes
25
replies
69k
views
14 follow
Tutorial:
Piping With Samtools, Bwa And Bedtools
unix
samtools
bwa
bedtools
updated 11 weeks ago by
Ram
36k • written 10.2 years ago by
Ying W
★ 4.1k
58
votes
25
replies
34k
views
15 follow
Tutorial:
Protocol To Downlad TCGA Data From GDC
GDC
TCGA
Download
methylation
Tutorial
updated 3.6 years ago by
ATpoint
62k • written 5.9 years ago by
Shicheng Guo
★ 9.1k
94
votes
25
replies
30k
views
11 follow
Tutorial:
Fastq Quality Control Shootout
quality
fastq
trimming
qc
tutorial
Tutorial
updated 3 months ago by
Ram
36k • written 9.8 years ago by
Istvan Albert
93k
9
votes
23
replies
7.6k
views
7 follow
Tutorial:
OrthoMCL installation on Ubuntu Linux
orthomcl
ubuntu
linux
mysql
Tutorial
4.1 years ago by
vimalkvn
▴ 310
141
votes
21
replies
28k
views
12 follow
Tutorial:
A few words for R beginners
Swirl
R
updated 7 weeks ago by
Ram
36k • written 7.5 years ago by
Parham
★ 1.6k
11
votes
20
replies
9.5k
views
10 follow
Tutorial:
Associating VDJ clonotyping data with scRNA-seq in Seurat
seurat
single cell
RNA-Seq
TCR
Tutorial
13 months ago by
jared.andrews07
★ 13k
8
votes
19
replies
12k
views
9 follow
Tutorial:
A:orthomcl with local mysql server on linux server, complete install
orthomcl
mysql
no root
local
Tutorial
updated 4 months ago by
Ram
36k • written 7.6 years ago by
Lesley Sitter
▴ 580
86
votes
19
replies
29k
views
12 follow
Tutorial:
Machine Learning For Cancer Classification - Part 1 - Preparing The Data Sets
classification
microarray
expression
bioconductor
Tutorial
updated 5.5 years ago by
yuanjun.ma
• 0 • written 8.7 years ago by
Obi Griffith
19k
51
votes
19
replies
40k
views
6 follow
Tutorial:
Visualizing Chip-Seq Data Using Ucsc [Bigwig]
chip-seq
rna-seq
bigwig
visualization
ucsc
tutorial
Tutorial
updated 6.4 years ago by
Shicheng Guo
★ 9.1k • written 10.2 years ago by
Sukhi Singh
10k
23
votes
19
replies
5.1k
views
10 follow
Tutorial:
MutScan: Detect important mutations by scanning FastQ files directly
mutation
fastq
cancer
target
Tutorial
updated 4.4 years ago by
lebedana21
• 0 • written 5.7 years ago by
chen
★ 2.4k
70
votes
19
replies
9.3k
views
15 follow
Tutorial:
Gene Set Enrichment Analysis
enrichment
microarray
Tutorial
GSEA
RNA-Seq
8 weeks ago by
Hamid Ghaedi
★ 2.5k
42
votes
19
replies
6.8k
views
8 follow
Tutorial:
Designing Command-Line Interfaces (Clis) For Scientific Software
software
tutorial
Tutorial
9.3 years ago by
Daniel Standage
4.0k
47
votes
19
replies
11k
views
8 follow
Tutorial:
Fastq Quality Control And Reporting - Aka Fastqc Versus The New Contenders
fastqc
qualitycontrol
tutorial
Tutorial
updated 9.3 years ago by
assafgordon
▴ 140 • written 9.3 years ago by
Istvan Albert
93k
8
votes
17
replies
2.1k
views
Tutorial:
Simple approach to RNA-seq (T-Bioinfo platform)
Tutorials
RNA-seq
alignment
next-gen
sequencing
6.7 years ago by
elia.brodsky
▴ 340
15
votes
17
replies
5.3k
views
9 follow
Tutorial:
Create de novo repeat library
Tutorial
repeat
annotation
de-novo
updated 10 months ago by
tshittu
• 0 • written 2.6 years ago by
Juke34
★ 7.1k
26
votes
17
replies
6.1k
views
8 follow
Tutorial:
virtualenv - running Python based software in isolation
python
virtualenv
updated 6 months ago by
Ram
36k • written 7.9 years ago by
Ian
5.8k
12
votes
17
replies
2.0k
views
Tutorial:
How to find the mapping percentages for data deposited in the Zaire ebolavirus bioproject from the 2014 outbreak
ebola
bwa
Tutorial
7.0 years ago by
Istvan Albert
93k
42
votes
16
replies
20k
views
15 follow
Tutorial:
Tutorial: Analyze exome Copy number variation (CNV) in single patient or in population.
CNV
varscan2
GISTIC
copy-number
Tutorial
written 6.8 years ago by
Chirag Nepal
★ 2.3k
98
votes
16
replies
27k
views
18 follow
Tutorial:
Heatmaps in R
Tutorial
R
heatmap
7 weeks ago by
Jean-Karim Heriche
25k
69
votes
16
replies
58k
views
10 follow
Tutorial:
How to Install SamTools, HTSLib, and BCFTools on Ubuntu 18.04
samtools
bcftools
htslib
Tutorial
updated 6 months ago by
jwalewski
• 0 • written 3.9 years ago by
otwtgin2010
▴ 460
32
votes
16
replies
14k
views
10 follow
Tutorial:
Machine Learning For Cancer Classification - Part 3 - Predicting With A Random Forest Classifier
classification
tutorial
Tutorial
5.2 years ago by
Obi Griffith
19k
34
votes
15
replies
17k
views
12 follow
Tutorial:
TCGA UUIDS to TCGA barcode (SampleID) in R
R
TCGA
GDC
next-gen
Tutorial
updated 3.3 years ago by
david.peeney
▴ 30 • written 5.7 years ago by
martinguerrerog89
▴ 310
24
votes
15
replies
7.4k
views
8 follow
Tutorial:
Syllabus To Learn Bioinformatics From Online Video Resources
bioinformatics
training
tutorial
Tutorial
3 months ago by
Medhat
9.3k
34
votes
15
replies
3.9k
views
6 follow
Tutorial:
How to do data cleaning for VCF genetic file
vcf
Tutorial
updated 3 months ago by
Ram
36k • written 3.0 years ago by
Shicheng Guo
★ 9.1k
57
votes
15
replies
9.8k
views
Tutorial:
Which human reference genome should I use?
genome
alignment
assembly
Tutorial
3.6 years ago by
finswimmer
15k
30
votes
14
replies
14k
views
8 follow
Tutorial:
Installation of the MuSiC suite on unsupported Linux distributions
install
genome
music
linux
smg
Tutorial
5.7 years ago by
Cyriac Kandoth
5.8k
348 results • Page
1 of 7
Recent Votes
Answer: ESTIMATE tumor purity
C: Run PHI-BLAST in BLAST+ standalone
Answer: Junior bioinformatician in italy
Junior bioinformatician in italy
A: Thoughts on switching from Biology to Bioinformatics
The Biostar Handbook. A bioinformatics e-book for beginners.
The Biostar Handbook. A bioinformatics e-book for beginners.
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Recent Awards •
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▴ 290
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Recent Replies
Answer: ESTIMATE tumor purity
by
JACKY
▴ 10
Just in case anyone faces this problem in the future, here is the link for the updated `estimate package` on github: https://github.com/…
Answer: Exctract unmapped reads from BLAST
by
GenoMax
117k
> Is there a way to tell blast to output the unmapped reads into a > separate file? No there is not. You will need to use `-outfmt 7` whe…
Comment: Resfams Database usage
by
Neel
▴ 10
Hi, i have annotated genome by prokka and o want to search amr agaisnt resfams could you please tell me how to do it steps by steps.
Comment: Exctract unmapped reads from BLAST
by
Pierre Lindenbaum
146k
those are two distinct commands https://linux.die.net/man/1/comm and https://linux.die.net/man/1/join extract the names of your queries, s…
Comment: Exctract unmapped reads from BLAST
by
Pilar
• 0
Thanks for answering :), sorry, I'm new at this. These are commands I should use when I launch Blast in terminal?
Comment: Exctract unmapped reads from BLAST
by
Pierre Lindenbaum
146k
have a look at `comm` or `join`.
Comment: Computing allele frequencies per individual for a set of SNPs in PLINK
by
pifferdavide
▴ 100
Sorry I forgot to mention I used it in this loop, which worked with another plink file, but not with this 1KG file. for popfile in $(l…
Comment: Computing allele frequencies per individual for a set of SNPs in PLINK
by
chrchang523
9.3k
`--indv` takes a single ID, not a filename. So `--indv IDlist.txt` shouldn't work.
Answer: Quast Ouput
by
Ying
• 0
The "# contigs 47484" is based on contig of size >= 500 bp (see the first line of your screenshot). The "# contigs (>= 0 bp)" is the raw nu…
Answer: SRA obtained metagenomic reads appears to corrupt - cannot work on SingleM
by
Mensur Dlakic
★ 19k
Not sure why: 1) you are splitting reads; 2) you are fixing reads when they seem fine. I suggest something like this instead after `prefetc…
Comment: Quick way to get a field such as QNAME from the last read in a bam file?
by
kalavattam
▴ 70
Thank you. Do you know of any strategies for non-coordinated-sorted bam files?
Comment: analyzing a single cell and searching for a specific gene using single cell data
by
jared.andrews07
★ 13k
@rpolicastro gave you several helpful links for using the h5ad file, in addition to how to explore and plot data. The links in my answer al…
Comment: Computing allele frequencies per individual for a set of SNPs in PLINK
by
pifferdavide
▴ 100
I was able to run the --indv command successfully on a file with a bed file by simply listing the IDs in single column. However, with anoth…
Answer: Get nucleotide sequence of assembled RNA transcripts
by
tomas4482
▴ 140
1. design a RNA-seq experiment specifically seuqencing non-coding RNA/circRNA sequencing. 2. subset to interested region -> extract chi…
Comment: gffcompare
by
linjc.xmu
▴ 30
Thanks. I revised it. Do you know how to achieve it?
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