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733 results • Page
1 of 15
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Views
Votes
Replies
362
votes
82
replies
144k
views
35 follow
Tool:
Gnu Parallel - Parallelize Serial Command Line Programs Without Changing Them
parallel
next-gen
ngs
updated 5 weeks ago by
jena
▴ 290 • written 11.2 years ago by
ole.tange
★ 4.4k
231
votes
38
replies
146k
views
29 follow
Tool:
Converting Genome Coordinates From One Genome Version To Another (Ucsc Liftover, Ncbi Remap, Ensembl Api)
ensembl
genome-coordinates
liftover
updated 10 months ago by
Ram
43k • written 11.2 years ago by
Malachi Griffith
19k
128
votes
83
replies
13k
views
8 follow
Tool:
Lossless ALAPY Fastq Compressor (now for MacOS X with 10-20% improved speed and compression ratio)
lossless-fastq-compression
fastq-compressor
updated 10 months ago by
Ram
43k • written 7.1 years ago by
Petr Ponomarenko
★ 2.8k
83
votes
46
replies
9.0k
views
15 follow
Tool:
ChatGPT optimized for bioinformatics questions
gpt
updated 7 weeks ago by
LauferVA
4.2k • written 11 months ago by
Sasha
▴ 840
79
votes
86
replies
32k
views
20 follow
Tool:
Introducing Clumpify: Create 30% Smaller, Faster Gzipped Fastq Files. And remove duplicates.
clumpify
storage
bbmap
pigz
compression
updated 10 months ago by
Ram
43k • written 7.4 years ago by
Brian Bushnell
20k
76
votes
14
replies
13k
views
10 follow
Tool:
karyoploteR: uncircle your genomes
karyoploteR
Rdataviz
NGS
updated 10 months ago by
Ram
43k • written 6.9 years ago by
bernatgel
★ 3.4k
72
votes
71
replies
31k
views
17 follow
Tool:
EnhancedVolcano: Publication-ready volcano plots with enhanced colouring and labeling
volcano-plot
bioconductor
ggplot2
ggrepel
updated 10 months ago by
Ram
43k • written 5.7 years ago by
Kevin Blighe
87k
68
votes
25
replies
16k
views
12 follow
Tool:
sra-explorer : find SRA and FastQ download URLs in a couple of clicks
fastq
SRA
updated 6 months ago by
GenoMax
142k • written 5.2 years ago by
Phil Ewels
★ 1.4k
61
votes
51
replies
22k
views
9 follow
Tool:
Efficiently process (view, analize, clip ends, convert, demultiplex, dereplicate) SFF/FastQ files
sff
sequence
fastq
next-gen
updated 10 months ago by
Ram
43k • written 10.0 years ago by
BioApps
▴ 790
56
votes
23
replies
5.1k
views
10 follow
Tool:
ASCIIGenome: Text Only Genome Viewer!
terminal
genome-browser
java
ASCIIGenome
updated 10 months ago by
Ram
43k • written 7.8 years ago by
dariober
14k
56
votes
52
replies
50k
views
12 follow
Tool:
Gene Set Clustering based on Functional annotation (GeneSCF)
geneSCF
Gene-Clustering
updated 10 months ago by
Ram
43k • written 9.8 years ago by
EagleEye
7.5k
54
votes
7
replies
4.0k
views
6 follow
Tool:
Looking For People That Would Try A Custom Genome Viewer That I Wrote For Bioinformatics
genome-viewer
updated 10 months ago by
Ram
43k • written 11.0 years ago by
chbelhumeur2000
▴ 40
54
votes
13
replies
10k
views
6 follow
Tool:
Bedtools: Analyzing Genomic Features
bedtools
updated 10 months ago by
Ram
43k • written 12.0 years ago by
Istvan Albert
100k
53
votes
6
replies
9.8k
views
8 follow
Tool:
list of dockerized bioinformatics apps
docker
updated 2.3 years ago by
Ram
43k • written 9.5 years ago by
14134125465346445
★ 3.6k
53
votes
13
replies
5.6k
views
6 follow
Tool:
I made a DNA/gene/bioinformatics-y workshop for 11-16 year olds which people may find useful
school-outreach
updated 16 months ago by
Ram
43k • written 8.9 years ago by
Daniel
★ 4.0k
50
votes
16
replies
14k
views
12 follow
Tool:
Omictools: A didactic directory for omic data analysis (NGS, microarray, PCR, MS, NMR)
pcr
software
ngs
updated 10 months ago by
Ram
43k • written 10.6 years ago by
arnaud.desfeux
▴ 450
48
votes
24
replies
8.2k
views
14 follow
Tool:
Hera: A new tool for RNA-Seq analysis
kallisto
RNA-Seq
STAR
gene-fusion
updated 10 months ago by
Ram
43k • written 6.8 years ago by
sonpham
▴ 580
46
votes
9
replies
43k
views
7 follow
Tool:
Tools to merge overlapping paired-end reads
ngs
Assembly
fastq
updated 13 months ago by
Charles-Alexandre Roy
▴ 50 • written 7.4 years ago by
Abdul Rafay Khan
★ 1.2k
38
votes
19
replies
11k
views
Tool:
Excel add-in for DNA/RNA string manipulations
sequence
DNA
RNA
Excel
updated 10 months ago by
Ram
43k • written 8.2 years ago by
jgbaum
▴ 140
38
votes
21
replies
19k
views
8 follow
Tool:
pybam - 100% python BAM reader
python
htspython
bam
pysam
updated 10 months ago by
Ram
43k • written 8.1 years ago by
John
13k
34
votes
9
replies
11k
views
7 follow
Tool:
Bwa-Meth: Align And Tabulate Bs-Seq Reads
methylation
updated 10 months ago by
Ram
43k • written 10.2 years ago by
brentp
24k
34
votes
30
replies
3.0k
views
6 follow
Tool:
BioFlows - Container-enabled Bioinformatics pipeline engine
workflow
next-gen
RNA-Seq
pipeline
updated 13 months ago by
Ram
43k • written 3.4 years ago by
drsami
▴ 90
33
votes
3
replies
15k
views
Tool:
Aligning Sequence Reads, Clone Sequences And Assembly Contigs With Bwa-Mem
bwa
ngs
updated 10 months ago by
Ram
43k • written 11.1 years ago by
lh3
33k
32
votes
6
replies
12k
views
Tool:
FASTA and FASTQ tools
Cpp
FASTA
Python
FASTQ
updated 16 months ago by
Ram
43k • written 8.9 years ago by
Kamil
★ 2.3k
31
votes
22
replies
13k
views
6 follow
Tool:
SeqKit: a cross-platform and ultrafast toolkit for FASTA/Q file manipulation in Golang
FASTQ
SeqKit
FASTA
updated 10 months ago by
Ram
43k • written 7.6 years ago by
shenwei356
8.5k
31
votes
30
replies
15k
views
6 follow
Tool:
BioVinci: user-friendly software to make plotting easy - PCA, 3D scatter plot, venn diagram, you name it.
gene
RNA-Seq
Venn-diagram
PCA
updated 10 months ago by
Ram
43k • written 6.0 years ago by
Jennifer Pham
▴ 450
30
votes
15
replies
10k
views
7 follow
Tool:
Snakemake--Python-Based Workflow Management
workflow
snakemake
python
updated 10 months ago by
Ram
43k • written 10.4 years ago by
Sean Davis
26k
29
votes
20
replies
3.7k
views
Tool:
FastQt : a clone of FastQC in C++/Qt
fastqc
Cpp
fastq
Qt
updated 10 months ago by
Ram
43k • written 7.4 years ago by
sacha
★ 2.4k
29
votes
29
replies
3.5k
views
6 follow
Tool:
weld (former brew) - yet another fastq utility
illlumina
python
updated 21 months ago by
Ram
43k • written 8.2 years ago by
tinysnippets
▴ 40
28
votes
7
replies
11k
views
Tool:
Quast Is A Convenient Tool For Assembly Evaluation
assembly
quality
updated 10 months ago by
Ram
43k • written 11.2 years ago by
Nikolay Vyahhi
★ 1.3k
28
votes
4
replies
15k
views
Tool:
Plotting GSEA output in R
RNA-Seq
javaGSEA
GSEA
updated 10 months ago by
Ram
43k • written 7.7 years ago by
thomaskuilman
▴ 850
28
votes
17
replies
5.1k
views
7 follow
Tool:
PCAtools: everything Principal Components Analysis
eigenvector
pca
bioconductor
R
updated 10 months ago by
Ram
43k • written 5.2 years ago by
Kevin Blighe
87k
27
votes
13
replies
6.0k
views
Tool:
DEA.R: Command line script for differential expression analysis with R packages (DESeq2/edgeR/limma-voom)
edgeR
DESeq2
limma
RNA-Seq
updated 10 months ago by
Ram
43k • written 7.8 years ago by
WouterDeCoster
47k
27
votes
12
replies
11k
views
Tool:
Skewer: a fast and accurate adapter trimmer for next-generation sequencing paired-end reads.
QC
Trimming
Read
Trimmer
updated 2.5 years ago by
Ram
43k • written 9.9 years ago by
Malachi Griffith
19k
27
votes
5
replies
1.9k
views
6 follow
Tool:
Efficient querying of genomic reference databases with gget
ensembl
enrichr
ncbi
gget
uniprot
updated 23 months ago by
Lior Pachter
▴ 700 • written 23 months ago by
Laura Luebbert
▴ 450
27
votes
6
replies
16k
views
Tool:
Bioawk - Fasta, Fastq, Sam, Bed, Gff Aware Awk Programming
awk
updated 10 months ago by
Ram
43k • written 11.9 years ago by
Istvan Albert
100k
26
votes
4
replies
5.3k
views
Tool:
Dgidb - Mining The Druggable Genome
dgidb
drug-gene-interaction
updated 10 months ago by
Ram
43k • written 10.6 years ago by
Obi Griffith
20k
26
votes
50
replies
14k
views
8 follow
Tool:
Retrieve a subset of FASTA from large Illumina multi-FASTA file
fasta
multi-fasta
illumina
updated 10 months ago by
Ram
43k • written 7.9 years ago by
hcwang
▴ 50
26
votes
22
replies
14k
views
10 follow
Tool:
BBSketch - A Tool for Rapid Sequence Comparison
minhash
sketch
bbmap
blast
updated 11 months ago by
Ram
43k • written 7.3 years ago by
Brian Bushnell
20k
26
votes
4
replies
3.3k
views
Tool:
LabWorm - a new CrowdSourcing platform for finding the newest & best bioinformatic tools
LabWorm
updated 13 months ago by
Ram
43k • written 7.9 years ago by
roy.granit
▴ 880
25
votes
19
replies
8.2k
views
10 follow
Tool:
pathfindR - Enrichment Analysis using Active Subnetworks
subnetwork
R
pathway-enrichment
updated 10 months ago by
Ram
43k • written 6.2 years ago by
egeulgen
★ 1.3k
25
votes
3
replies
4.9k
views
Tool:
Quick statistics from the command line
statistics
C
updated 17 months ago by
Ram
43k • written 8.8 years ago by
Kamil
★ 2.3k
25
votes
17
replies
17k
views
Tool:
HeatmapGenerator: High performance RNAseq and microarray visualization software suite to examine differential gene expression levels using an R and C…
heatmap
microarray
R
Cpp
RNA-Seq
updated 2.1 years ago by
Ram
43k • written 9.4 years ago by
Bohdan Khomtchouk
▴ 350
24
votes
26
replies
3.7k
views
Tool:
ClinCNV: CNV detection from short reads
variant-calling
cna
cnv
updated 10 months ago by
Ram
43k • written 4.6 years ago by
German.M.Demidov
★ 2.9k
23
votes
19
replies
4.3k
views
7 follow
Tool:
Big Browser : a new genom browser in development
genome-browser
updated 10 months ago by
Ram
43k • written 8.2 years ago by
sacha
★ 2.4k
23
votes
10
replies
12k
views
Tool:
ggtree: phylogenetic tree visualization and annotation
ggtree
phylogeny
visualization
updated 10 months ago by
Ram
43k • written 7.8 years ago by
Guangchuang Yu
★ 2.6k
22
votes
20
replies
4.8k
views
Tool:
elPrep 4.0.0, a high-performance drop-in replacement tool for GATK4/Picard/SAMtools for processing SAM/BAM files
sam
bam
bqsr
updated 10 months ago by
Ram
43k • written 5.5 years ago by
Charlotte.Herzeel
▴ 150
22
votes
8
replies
6.6k
views
Tool:
BioTuring Browser: Making single-cell sequencing data in published studies really accessible!
scRNA-Seq
single-cell
updated 10 months ago by
Ram
43k • written 5.6 years ago by
sonpham
▴ 580
22
votes
22
replies
18k
views
Tool:
Pan-Cancer Analysis And Networks Of LncRNAs, MiRNAs, circRNAs, CeRNAs And RNA-Binding Proteins From TCGA 32 Cancer Types and CLIP-seq data
cancer
TCGA
RNA-Binding-Proteins
miRNA
lncRNA
updated 19 months ago by
Ram
43k • written 10.2 years ago by
lsp03yjh
▴ 860
22
votes
5
replies
8.4k
views
Tool:
Salmon: A fast and versatile new tool for RNA-seq quantification
RNA-Seq
updated 2.2 years ago by
Ram
43k • written 9.4 years ago by
Rob
6.5k
733 results • Page
1 of 15
Recent Votes
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Meme-Tools: Bit score
Meme-Tools: Bit score
Comment: error in R code
DEXSeq multiple time points
How to find the most frequent alternative-splicing event from DEXSEQ data?
Comment: Design matrix Differential expression analysis
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Recent Replies
Answer: Quetion regarding WGCNA
by
deepak180001
• 0
Thank you for your reply andres.firrincieli. I have attached the PCA plot of the expression data used in the WGCNA. ![enter imag…
Comment: Design matrix Differential expression analysis
by
SHN
▴ 40
Got it, thank you for your response. SN
Comment: How to interpret DEXseq results in therms of significance
by
Sara
▴ 30
Hi, I used write.table(as.data.frame(DEXSeqResults(MyObj)), "Results.tsv", quote=FALSE, sep="\t", dec=".") to save the result but I recei…
Comment: Tissue-specific DEG analysis with DEseq2
by
M.
▴ 30
Can I ask what do you exactly mean by same experiment? If you are talking about the same donor and the same procedure, unfortunately, not a…
Comment: install package: package ‘gmwm’ is not available for this version of R
by
Ram
43k
Find someone with computer skills near you and consult them. From your posts on the forum, it's clear that you need help at a level that we…
Comment: Gene Specific coverage from WGS data
by
GenoMax
142k
This is not going to work no matter what program you use since the chromosome identifiers in your GTF (`MN908947.3 `) do not match your BA…
Comment: install.packages("imudata") - package ‘imudata’ is not available for this versio
by
Ram
43k
Read the answers in the post, understand them and try to implement them.
Comment: High Malat-1 expression in single cell data
by
t.montserrat.ayuso
▴ 10
Just using the normalized expression of Malat1 works.
Comment: Can I merge Hi-C fastq files from different lanes?
by
Winter
• 0
Awesome, thank you for the concise and straight-forward answer!
Comment: error in R code
by
ATpoint
82k
Look, before you keep posting these sorts of questions and might gross of users, please read and follow https://www.biostars.org/p/357878/ …
Comment: Gene Specific coverage from WGS data
by
1769mkc
★ 1.2k
"Also if is there any other quick way to find gene specific coverage" can you give some example so that its bit more clear what do you mean…
Answer: Tissue-specific DEG analysis with DEseq2
by
ATpoint
82k
I assume that all data are from the same experiment, without batch effects and can thus be quantitiatively compared: Many ways to do thi…
Comment: install.packages("imudata") - package ‘imudata’ is not available for this versio
by
snajafy
• 0
I am facing the same problem and I don't know how to solve the problem,....
Comment: install.packages("imudata")
by
zx8754
11k
[How should I deal with "package 'xxx' is not available (for R version x.y.z)" warning?](https://stackoverflow.com/q/25721884/680068)
Answer: install.packages("imudata")
by
ATpoint
82k
Welcome to this community. Please learn the most important lesson right away which is reading answers and learning from it. Users gave you …
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