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379 results • Page
1 of 8
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Votes
Replies
238
votes
176
replies
88k
views
73 follow
Tutorial:
Survival analysis of TCGA patients integrating gene expression (RNASeq) data
RNA-Seq
Survival
TCGA
updated 4 months ago by
Ram
40k • written 8.2 years ago by
TriS
★ 4.7k
132
votes
123
replies
33k
views
23 follow
Tutorial:
Survival analysis with gene expression
cox
gene-expression
survival-analysis
geo
updated 6 months ago by
1769mkc
★ 1.1k • written 4.9 years ago by
Kevin Blighe
86k
93
votes
105
replies
39k
views
25 follow
Tutorial:
Produce PCA bi-plot for 1000 Genomes Phase III - Version 2
1000genomes
PLINK
PCA
updated 6 months ago by
Ram
40k • written 5.1 years ago by
Kevin Blighe
86k
76
votes
70
replies
17k
views
18 follow
Tutorial:
Clustering of DAVID gene enrichment results from gene expression studies
enrichment
david
updated 6 months ago by
Ram
40k • written 5.6 years ago by
Kevin Blighe
86k
146
votes
70
replies
46k
views
20 follow
Tutorial:
Network plot from expression data in R using igraph
microarray
RNA-Seq
R
network
updated 4 weeks ago by
Raheleh
▴ 260 • written 5.9 years ago by
Kevin Blighe
86k
116
votes
66
replies
43k
views
20 follow
Tutorial:
[Deprecated] Fast download of FASTQ files from the European Nucleotide Archive (ENA)
aspera
fastq-dump
Fastq
ENA
updated 6 months ago by
Ram
40k • written 5.2 years ago by
ATpoint
77k
73
votes
60
replies
25k
views
16 follow
Tutorial:
Produce PCA bi-plot for 1000 Genomes Phase III in VCF format (old)
1000genomes
PLINK
PCA
VCF
updated 7 months ago by
Ram
40k • written 6.1 years ago by
Kevin Blighe
86k
60
votes
52
replies
41k
views
23 follow
Tutorial:
Creating Interactive Volcano Plots with R and Plot.ly
plotly
R
volcano-plot
updated 6 months ago by
Ram
40k • written 7.0 years ago by
steve
★ 3.3k
72
votes
48
replies
16k
views
15 follow
Tutorial:
For Short Reads, Which Aligners Find All Hits Given Certain Edit Distance Threshold?
ngs
alignment
bwa
updated 7 months ago by
Ram
40k • written 10.6 years ago by
lh3
33k
84
votes
47
replies
30k
views
28 follow
Tutorial:
Extract Total Non-Overlapping Exon Length Per Gene With Bioconductor
fpkm
rna-seq
bioconductor
updated 1 day ago by
Ram
40k • written 10.0 years ago by
Irsan
★ 7.7k
196
votes
44
replies
70k
views
33 follow
Tutorial:
Analysing Microarray Data In Bioconductor
microarray-analysis
bioconductor
updated 8 months ago by
Ram
40k • written 11.0 years ago by
Obi Griffith
20k
59
votes
43
replies
19k
views
18 follow
Tutorial:
Polish PacBio assembly with latest PacBio tools : an affordable solution for everyone
pbalign
pacbio
arrow
smrt-limk
updated 6 months ago by
Ram
40k • written 6.0 years ago by
Rox
★ 1.4k
18
votes
40
replies
17k
views
16 follow
Tutorial:
Easy way to run easily orthoMCL (Copy & paste)
all-v-all
orthomcl
updated 6 months ago by
Ram
40k • written 7.3 years ago by
Esaie
▴ 170
282
votes
39
replies
174k
views
29 follow
Tutorial:
How to download raw sequence data from GEO/SRA
fastq
SRA
bam
GEO
updated 6 months ago by
Ram
40k • written 9.1 years ago by
Obi Griffith
20k
149
votes
35
replies
60k
views
33 follow
Tutorial:
Tools For Metagenomic Data Analysis
metagenomics
next-gen
updated 7 months ago by
Ram
40k • written 10.8 years ago by
vijay
★ 1.6k
83
votes
34
replies
17k
views
22 follow
Tutorial:
Enrichment Analysis, Clustering and Scoring with pathfindR
enrichment
R
pathway
active-subnetwork
updated 4 months ago by
adelheidkratzer
• 0 • written 5.3 years ago by
egeulgen
★ 1.3k
146
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 7 months ago by
Ram
40k • written 10.5 years ago by
Cyriac Kandoth
6.0k
288
votes
33
replies
99k
views
25 follow
Tutorial:
Cheat Sheet For One-Based Vs Zero-Based Coordinate Systems
coordinates
updated 7 months ago by
Ram
40k • written 9.9 years ago by
Obi Griffith
20k
13
votes
31
replies
5.7k
views
6 follow
Tutorial:
gene set filter/selection for training ab initio annotation tools
geneset
genome
gene
abinitio
updated 6 months ago by
Ram
40k • written 4.1 years ago by
Juke34
8.2k
84
votes
29
replies
30k
views
20 follow
Tutorial:
How to create a mutation landscape (waterfall) plot with GenVisR
BioConductor
GenVisR
Graphics
R
updated 9 weeks ago by
amziepickles
• 0 • written 7.6 years ago by
Obi Griffith
20k
48
votes
28
replies
8.6k
views
9 follow
Tutorial:
How to Use Biostars, Part-I: Questions, Answers, Comments and Replies
documentation
meta
how-to
4 months ago by
Ram
40k
64
votes
26
replies
12k
views
7 follow
Tutorial:
Parallel processing in R
biocparallel
mclapply
foreach
R
updated 6 months ago by
Ram
40k • written 6.0 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 6 months ago by
Ram
40k • written 4.6 years ago by
finswimmer
16k
71
votes
26
replies
26k
views
15 follow
Tutorial:
How To Separate Illumina Based Strand Specific Rna-Seq Alignments By Strand
RNA-seq
updated 7 months ago by
Ram
40k • written 9.6 years ago by
Istvan Albert
98k
58
votes
25
replies
38k
views
15 follow
Tutorial:
Protocol To Downlad TCGA Data From GDC
GDC
methylation
TCGA
updated 6 months ago by
Ram
40k • written 7.2 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 7 months ago by
Ram
40k • written 11.0 years ago by
Istvan Albert
98k
137
votes
25
replies
80k
views
14 follow
Tutorial:
Piping With Samtools, Bwa And Bedtools
unix
samtools
bwa
bedtools
updated 18 months ago by
Ram
40k • written 11.4 years ago by
Ying W
★ 4.2k
9
votes
23
replies
9.1k
views
7 follow
Tutorial:
OrthoMCL installation on Ubuntu Linux
ubuntu
orthomcl
mysql
linux
updated 4 months ago by
Ram
40k • written 5.7 years ago by
vimalkvn
▴ 310
86
votes
22
replies
80k
views
14 follow
Tutorial:
How to Install SamTools, HTSLib, and BCFTools on Ubuntu 18.04
bcftools
samtools
htslib
updated 11 weeks ago by
sifa.khan
• 0 • written 5.2 years ago by
otwtgin2010
▴ 580
18
votes
22
replies
8.1k
views
10 follow
Tutorial:
Create de novo repeat library
de-novo
repeat
annotation
updated 6 days ago by
evoecogen
▴ 20 • written 3.8 years ago by
Juke34
8.2k
84
votes
21
replies
19k
views
16 follow
Tutorial:
Gene Set Enrichment Analysis
microarray
enrichment
RNA-Seq
GSEA
updated 6 months ago by
Ram
40k • written 3.0 years ago by
Hamid Ghaedi
3.0k
142
votes
21
replies
29k
views
12 follow
Tutorial:
A few words for R beginners
Swirl
R
updated 17 months ago by
Ram
40k • written 8.8 years ago by
Parham
★ 1.6k
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 6 months ago by
Ram
40k • written 4.3 years ago by
jared.andrews07
★ 15k
42
votes
19
replies
7.4k
views
8 follow
Tutorial:
Designing Command-Line Interfaces (Clis) For Scientific Software
software
updated 7 months ago by
Ram
40k • written 10.6 years ago by
Daniel Standage
4.1k
23
votes
19
replies
6.1k
views
10 follow
Tutorial:
MutScan: Detect important mutations by scanning FastQ files directly
fastq
mutation
cancer
target
updated 5 months ago by
Ram
40k • written 7.0 years ago by
chen
★ 2.4k
8
votes
19
replies
12k
views
9 follow
Tutorial:
A:orthomcl with local mysql server on linux server, complete install
mysql
orthomcl
updated 6 months ago by
Ram
40k • written 8.9 years ago by
Lesley Sitter
▴ 590
53
votes
19
replies
42k
views
6 follow
Tutorial:
Visualizing Chip-Seq Data Using Ucsc [Bigwig]
visualization
bigwig
chip-seq
rna-seq
updated 7 months ago by
Ram
40k • written 11.5 years ago by
Sukhi Singh
11k
47
votes
19
replies
13k
views
8 follow
Tutorial:
Fastq Quality Control And Reporting - Aka Fastqc Versus The New Contenders
quality-control
fastqc
updated 8 months ago by
Ram
40k • written 10.6 years ago by
Istvan Albert
98k
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 7 months ago by
Ram
40k • written 9.9 years ago by
Obi Griffith
20k
26
votes
17
replies
7.1k
views
8 follow
Tutorial:
virtualenv - running Python based software in isolation
python
virtualenv
updated 12 months ago by
Ram
40k • written 9.1 years ago by
Ian
6.0k
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 4 months ago by
GenoMax
134k • written 9.9 years ago by
Obi Griffith
20k
12
votes
17
replies
2.5k
views
Tutorial:
How to find the mapping percentages for data deposited in the Zaire ebolavirus bioproject from the 2014 outbreak
ebola
bwa
updated 9 months ago by
Ram
40k • written 8.3 years ago by
Istvan Albert
98k
8
votes
17
replies
2.7k
views
Tutorial:
Simple approach to RNA-seq (T-Bioinfo platform)
alignment
next-gen-sequencing
RNA-seq
updated 13 months ago by
Ram
40k • written 8.0 years ago by
elia.brodsky
▴ 340
42
votes
16
replies
22k
views
15 follow
Tutorial:
Tutorial: Analyze exome Copy number variation (CNV) in single patient or in population.
GISTIC
varscan2
CNV
copy-number
updated 13 months ago by
Ram
40k • written 8.0 years ago by
Chirag Nepal
★ 2.4k
99
votes
16
replies
32k
views
18 follow
Tutorial:
Heatmaps in R
heatmap
R
updated 6 months ago by
Ram
40k • written 7.2 years ago by
Jean-Karim Heriche
26k
25
votes
15
replies
8.4k
views
8 follow
Tutorial:
Syllabus To Learn Bioinformatics From Online Video Resources
course
training
mooc
updated 7 months ago by
Ram
40k • written 10.7 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 6 months ago by
Ram
40k • written 7.0 years ago by
martinguerrerog89
▴ 310
61
votes
15
replies
13k
views
Tutorial:
Which human reference genome should I use?
assembly
genome
alignment
updated 4 months ago by
Ram
40k • written 5.0 years ago by
finswimmer
16k
34
votes
15
replies
5.8k
views
6 follow
Tutorial:
How to do data cleaning for VCF genetic file
vcf
updated 6 months ago by
Ram
40k • written 4.3 years ago by
Shicheng Guo
★ 9.3k
20
votes
14
replies
3.6k
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 5 months ago by
Ram
40k • written 7.4 years ago by
Mads Lerdrup
▴ 460
379 results • Page
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Answer: Software Tool to Translate DNA to Protein
Comment: Frustrated with DEA results
Pedigree - Haplotype building and VCF files
A: Pedigree - Haplotype building and VCF files
A: Individual VCF files from main VCF file
Individual VCF files from main VCF file
A: Splitting vcf files to individual samples
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Comment: Why should ATAC-seq mapped reads be shifted +4 and -5 for +strand and -strand, r
by
ATpoint
77k
As I said above, it depends on how you count. IGV is 1-based, BED files are 0-based, so it depends on the coordinate system. On the molecul…
Answer: Why should ATAC-seq mapped reads be shifted +4 and -5 for +strand and -strand, r
by
suragnair
• 0
Turns out +4/-4 is the correct shift. You can see that when you make a bigwig separately from the + and - strands, then the reads align wit…
Answer: ATAC-seq +4 -5 shift
by
suragnair
• 0
Turns out +4/-4 is the correct shift. You can see that when you make a bigwig separately from the + and - strands, then the reads align wit…
Answer: Assessing Rockhopper's output
by
shelkmike
▴ 980
I didn't do *de novo* transcriptome assemblies with Rockhopper. Only reference-based analyses. However, having very long transcripts is nor…
Answer: Recommendations for extending contigs from denovo assembly to identify SV insert
by
shelkmike
▴ 980
Some time ago I made a tool Elloreas (https://github.com/shelkmike/Elloreas) that iteratively extends a contig using long reads. It can be …
Answer: How to get the gft file to run velocyto for velocity analysis?
by
ATpoint
77k
You need the same GTF file that was used during mapping of your 10x data. If you used CellRanger and it was mouse (given you used recent Ce…
Answer: Lower alignment rate when using collapsed reads
by
LChart
3.4k
Sequences are collapsed if they're sufficiently identical. Garbage (random) reads won't collapse. If you collapse the "good" reads and don'…
Comment: Complex multifactorial DE analysis with limma/edgeR based on rnaseq data
by
LChart
3.4k
(1) Yes; but you can simply subset the DESeq via `dds[,dds$donor != UNWANTED_DONOR]` (3) Given the initial results (and the MDS) that dono…
Comment: Unmapped Reads in Kallisto
by
dsull
★ 4.7k
Sounds good! I just added a solution here.
Answer: Unmapped Reads in Kallisto
by
dsull
★ 4.7k
Running kallisto bus with the -n option will record the read numbers of the reads that have been successfully mapped in the output BUS file…
Comment: Automate the Splitting of a VCF File by Sample (bcftools)
by
cfos4698
▴ 830
Just a comment re: your bash example reading from a file. Have you tried `while` instead of 'with'? ``` while read sample; do bcftools…
Comment: Split plink files by a number of SNPs
by
Raygozak
★ 1.4k
Out of curiosity, why would someone ask how to do something if they already knew how to do it or which tools to use? Also, the OP is not a…
Comment: Comparing multiple RNASeq studies
by
Zhenyu Zhang
▴ 980
no. The best you can do is to draw conclusion using one dataset, and validate your conclusion using other datasets.
Comment: comparision of umap single cell
by
synat.keam
▴ 80
Thank, Seniors.. I figured out the issue of my integration as I did not state the ``` reduction= "harmony" ```
Comment: Issue with merging in plink and eigensoft.
by
bk11
★ 1.2k
> I merged two datasets in plink1.9. It worked, but I did get the error > "multiple positions seen for variant" and "variants have the same…
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