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736 results • Page
3 of 15
Sort: Votes
Rank
Views
Votes
Replies
13
votes
14
replies
2.3k
views
Tool:
Collaboration on an empirical QC tool
RNA-Seq
QC
sequencing
updated 10 months ago by
Ram
43k • written 7.0 years ago by
Michael
54k
12
votes
3
replies
2.8k
views
Tool:
Hiplot: a simple and user-friendly visualization platform for scientific data
R
microbial
RNA-Seq
visualization
updated 11 months ago by
Ram
43k • written 3.8 years ago by
Hiplot
▴ 130
12
votes
6
replies
3.5k
views
Tool:
Variant annotation and filtration server ALAPY Genome Explorer (AGx)
vcf
variant-annotation
variant-interpretation
updated 10 months ago by
Ram
43k • written 7.0 years ago by
Petr Ponomarenko
★ 2.8k
12
votes
3
replies
3.1k
views
Tool:
The Biopieces Are A Collection Of Bioinformatics Tools
sequence
updated 10 months ago by
Ram
43k • written 11.3 years ago by
Medhat
9.7k
12
votes
5
replies
3.6k
views
Tool:
Kitten - A DNA Sequence Dereplicator & Cluster Viewer (GUI)
dereplication
sequence
nextgen
clustering
updated 2.4 years ago by
Ram
43k • written 9.7 years ago by
BioApps
▴ 790
12
votes
5
replies
6.2k
views
Tool:
AGAT - Another Gff/Gtf Analysis Toolkit
gff
gtf
updated 10 months ago by
Ram
43k • written 4.4 years ago by
Juke34
8.6k
12
votes
8
replies
3.2k
views
Tool:
BioBit: Global bioinformatics chat
communication
updated 13 months ago by
Ram
43k • written 7.9 years ago by
vadim.nazarov
▴ 90
12
votes
1
reply
2.7k
views
Tool:
iStack: an R solution for plotting stacked bars using custom icons
R
updated 11 months ago by
Ram
43k • written 5.4 years ago by
brettgao2018
▴ 150
12
votes
5
replies
3.6k
views
Tool:
biomartian enables querying BioMart from the command line - now all Python!
biomart
updated 19 months ago by
Ram
43k • written 8.8 years ago by
Endre Bakken Stovner
▴ 960
12
votes
4
replies
1.1k
views
Tool:
BBTools 39.03 released!
BBTools
BBMap
7 months ago by
Brian Bushnell
20k
12
votes
9
replies
7.8k
views
Tool:
gogadget: an R package for go analysis visualization and interpretation
goseq
R
RNA-Seq
gogadget
updated 11 months ago by
Ram
43k • written 7.8 years ago by
Benn
8.3k
12
votes
7
replies
3.2k
views
Tool:
Chromozoom: The Genome Browser That Lets You Fly!
genome-browser
browser
updated 10 months ago by
Ram
43k • written 11.2 years ago by
Istvan Albert
100k
12
votes
0
replies
4.8k
views
Tool:
UMI-Tools 0.5, now with tools for cell barcoded scRNA-seq
UMI
RNA-Seq
single-cell
updated 11 months ago by
Ram
43k • written 6.7 years ago by
i.sudbery
19k
11
votes
2
replies
1.9k
views
Tool:
Tools, Resources, Training material from ISMB/ECCB, BOSC 2017
BOSC
ISMB
Resources
ECCB
updated 12 months ago by
Ram
43k • written 6.8 years ago by
venu
7.1k
11
votes
2
replies
781
views
Tool:
Pipeline Generator
gpt
updated 9 months ago by
LauferVA
4.2k • written 9 months ago by
Sasha
▴ 850
11
votes
10
replies
2.3k
views
Tool:
[Crushing the bureaucracy in bioinformatics] Introducing Skymap-JupyterHub: accessing and utilizing reprocessed expression/ allelic read count profil…
SNP
RNA-Seq
ChIP-Seq
updated 11 months ago by
Ram
43k • written 5.8 years ago by
btsui
▴ 300
11
votes
2
replies
13k
views
Tool:
Multiplex PCR Primer Design Tools
multiplex-PCR
updated 11 months ago by
Ram
43k • written 6.7 years ago by
Shicheng Guo
★ 9.4k
11
votes
12
replies
4.9k
views
Tool:
Mapsembler2 targeted micro assembly and visualization of the local assembly graph
minia
mapsembler
next-gen
Assembly
updated 2.1 years ago by
Ram
43k • written 9.8 years ago by
pierre.peterlongo
▴ 900
11
votes
7
replies
6.2k
views
Tool:
RNA Modification Database and Epitranscriptome Sequencing Data
Epitranscriptome
m5C
m6A
RNA-modification
m1A
updated 20 months ago by
Ram
43k • written 8.6 years ago by
lsp03yjh
▴ 860
11
votes
2
replies
2.7k
views
Tool:
Open Targets batch search, your list of human genes matched to our disease associations
Disease
Drug
Open-Targets
updated 12 months ago by
Ram
43k • written 7.0 years ago by
Denise CS
★ 5.2k
11
votes
3
replies
4.6k
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
11
votes
2
replies
7.1k
views
Tool:
fastp (the ultra-fast all-in-one FASTQ preprocessing tool) v0.18.0 released, 2X faster, with many new features.
fastp
QC
updated 11 months ago by
Ram
43k • written 5.9 years ago by
chen
★ 2.5k
11
votes
14
replies
6.5k
views
6 follow
Tool:
[share] Script to bulk retrieve DNA sequences by protein IDs from GenBank
python
genbank
sequence
cds
protein
updated 2.3 years ago by
Ram
43k • written 9.5 years ago by
qiyunzhu
▴ 130
11
votes
3
replies
2.8k
views
Tool:
Sequence Database curator
sequence
fastq
sequencing
blast
updated 11 months ago by
Ram
43k • written 7.3 years ago by
Eslam Samir
▴ 110
11
votes
2
replies
5.3k
views
Tool:
ChIPQC: a package for assessing quality of ChIP-seq samples and experiments
quality-control
quality-assessment
ChIP-Seq
updated 10 months ago by
Ram
43k • written 10.1 years ago by
Rory Stark
★ 2.0k
11
votes
1
reply
4.8k
views
Tool:
Ideogram.js: a JavaScript library for chromosome visualization
javascript
chromosome
visualization
ideogram
updated 11 months ago by
Ram
43k • written 6.2 years ago by
Eric Weitz
▴ 120
11
votes
0
replies
3.0k
views
Tool:
Pyblue: A Simple Tool To Generate Data/Code Oriented Static Web Sites (version 2.0 released)
pyblue
updated 10 months ago by
Ram
43k • written 10.8 years ago by
Istvan Albert
100k
11
votes
5
replies
2.6k
views
Tool:
A resource with diverse databases and tools for SARS-CoV-2 (COVID-19) bioinformatics -- Updates
SARS-CoV-2
Corona
Databases
COVID-19
updated 11 months ago by
Ram
43k • written 4.2 years ago by
Michael
▴ 270
10
votes
5
replies
2.5k
views
Tool:
Genozip: A new compression tool for FASTQ, BAM, VCF and more
bam
vcf
fastq
compression
10 months ago by
Divon
▴ 230
10
votes
2
replies
7.5k
views
Tool:
fastp, the ultra-fast FASTQ preprocessing tool, is now on BioConda
fastp
updated 14 months ago by
Ram
43k • written 6.4 years ago by
chen
★ 2.5k
10
votes
3
replies
6.3k
views
Tool:
GenVisR: Genomic Visualizations in R
visualization
genomic
RNA-Seq
genvisr
updated 11 months ago by
Ram
43k • written 7.9 years ago by
Obi Griffith
20k
10
votes
1
reply
7.5k
views
Tool:
Comb-P: Combining Spatially Correlated P-Values
methylation
updated 10 months ago by
Ram
43k • written 11.6 years ago by
brentp
24k
10
votes
12
replies
1.9k
views
Tool:
PanDepth, an ultra-fast and efficient genomic tool for coverage calculation
bam
paf
depth
cram
coverage
3 months ago by
Huiyang
▴ 190
10
votes
6
replies
5.7k
views
Tool:
Shell script to automate trimmomatic for multiple samples
bash
shell
trimmomatic
updated 11 months ago by
Ram
43k • written 5.0 years ago by
lakhujanivijay
5.8k
10
votes
0
replies
5.8k
views
Tool:
Shell utilities for QC of FASTQ/FASTA files (based on perl one-liners)
PERL
GNUPLOT
FASTA
FASTQ
FastQC
updated 10 months ago by
Ram
43k • written 10.1 years ago by
umer.zeeshan.ijaz
★ 1.8k
10
votes
8
replies
1.9k
views
6 follow
Tool:
"bioalcidae, samjs and vcffilterjs" published in bioinformatics.
jvarkit
bam
vcf
javascript
java
updated 11 months ago by
Ram
43k • written 6.5 years ago by
Pierre Lindenbaum
161k
10
votes
2
replies
2.1k
views
Tool:
Onezoom For Viewing Large Phylogenetic Tree Data
phylogeny
updated 10 months ago by
Ram
43k • written 11.6 years ago by
Mary
11k
10
votes
0
replies
2.7k
views
Tool:
Real Time Programming for Bioinformatics (and for fun)
coderscrowd
collaborative-editor
updated 14 months ago by
Ram
43k • written 9.8 years ago by
Rad
▴ 810
10
votes
1
reply
1.5k
views
Tool:
fastp 0.23.0 released, runs 2x faster, and generates reproducible outputs.
FASTQ
updated 2.6 years ago by
GenoMax
142k • written 2.6 years ago by
chen
★ 2.5k
9
votes
0
replies
9.2k
views
Tool:
Pyteomics - An Open-Source Python Framework For Mass Spectrometry (Ms) Based Proteomics
proteomics
python
mass-spec
sequence
updated 11 months ago by
Ram
43k • written 11.2 years ago by
lev.levitsky
▴ 90
9
votes
8
replies
3.8k
views
6 follow
Tool:
NCBI-SRA File Downloader
NCBI
sra
sequence
updated 14 months ago by
Ram
43k • written 8.7 years ago by
sanjay.deshpande
▴ 50
9
votes
4
replies
6.0k
views
Tool:
BPGA - Bacterial Pan Genome Analysis pipeline
sequence
genome
comparative-genomics
bacteria
updated 11 months ago by
Ram
43k • written 8.0 years ago by
bpgatool
▴ 80
9
votes
12
replies
4.6k
views
Tool:
fastp v0.9 released: an all-in-one FASTQ preprocessor (QC, adapters, trimming, quality filtering / cutting, splitting output ... )
fastq
fastp
open-source
updated 11 months ago by
Ram
43k • written 6.6 years ago by
chen
★ 2.5k
9
votes
9
replies
4.7k
views
Tool:
pyCirclize - Circular visualization in Python
visualization
circos
matplotlib
genome
python
updated 9 months ago by
shuo
• 0 • written 17 months ago by
moshi
▴ 150
9
votes
1
reply
7.0k
views
Tool:
Rsem: Accurate Transcript Quantification From Rna-Seq Data With Or Without A Reference Genome
rna-seq
RSEM
updated 10 months ago by
Ram
43k • written 11.7 years ago by
Istvan Albert
100k
9
votes
23
replies
9.8k
views
Tool:
BioLabDonkey - new Mac program for molecular biologists
software
biolabdonkey
7 days ago by
vytarasov
▴ 180
9
votes
4
replies
2.7k
views
Tool:
Compareads: Comparing Huge Metagenomic Experiments
metagenomics
denovo
next-gen
updated 10 months ago by
Ram
43k • written 11.3 years ago by
Nico
▴ 180
9
votes
2
replies
3.9k
views
Tool:
Patch ERCC spike sequences to get their real 5-prime ends.
spikes
ERCC
CAGE
updated 21 months ago by
Ram
43k • written 8.4 years ago by
Charles Plessy
★ 2.9k
9
votes
2
replies
3.8k
views
Tool:
BioPandas - Working with molecular structures in pandas DataFrames
protein-structure
protein-data-bank
pdb
updated 21 months ago by
Ram
43k • written 8.5 years ago by
se.raschka
▴ 150
9
votes
4
replies
2.3k
views
Tool:
SEDA (SEquence DAtaset builder): a desktop tool for processing FASTA files containing DNA and protein sequences
fasta
sequences
java
5 months ago by
Hugo
▴ 380
736 results • Page
3 of 15
Recent Votes
A: How is the design in DESeq2 work?
Error in CIBERSORTx ($ operator is invalid for atomic vectors)
Answer: RNAseq coverage vs depth for transcript isoform expression?
constructing pangenome through psvcp
Differential Expression with limma: Contrast and Design Matrix, combinatorial approach valid?
Differential Expression with limma: Contrast and Design Matrix, combinatorial approach valid?
Answer: RNAseq coverage vs depth for transcript isoform expression?
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Recent Replies
Comment: Error in CIBERSORTx ($ operator is invalid for atomic vectors)
by
nguyenn6
• 0
did you ever figure it out? i'm having the same issue.
Comment: Traveler with Infernal mapping failed
by
anton.i.petrov
• 0
Hi Larissa! I am the lead developer of R2DT and I've just noticed this question. Could you please email help@r2dt.bio with your input seque…
Comment: constructing pangenome through psvcp
by
analyst
▴ 50
Fixed the issue by updating nucmer version.
Comment: Blastn error : ncbi::CObject::ThrowNullPointerException() - Attempt to access NU
by
GenoMax
142k
Can you create a small test database (`makeblastdb`) from your query file and try to run the search against the same file and see if that w…
Comment: calculating genomic coverage/ base overlap in R
by
1769mkc
★ 1.2k
you can `dput(head(df)` for the both the data frame so that other can test for possible solutions
Comment: Broad and Narrow peaks
by
ATpoint
82k
What is your question? It's unclear.
Comment: Help with Biopython for Beginner
by
Joe
21k
One question before offering more solutions: are you trying to learn Python with this as an example problem, or are you trying to find the …
Answer: RNAseq coverage vs depth for transcript isoform expression?
by
Gordon Smyth
★ 7.2k
See the exploration of isoform estimation precision vs read length and sequencing depth in our paper: https://doi.org/10.1093/nar/gkad1167.…
Comment: How to handle duplicated genes in TCGA data?
by
txema.heredia
▴ 130
Why does the tool require gene symbols and not ensembl ids? Is it retrieving information from somewhere else? If so, your best bet is to fi…
Comment: how to treat the replicates while performing WGCNA
by
mavy
▴ 10
Thank you so much for your response . Really appreciate it. I will try the way you mentioned and will get back if I have any query
Comment: Blastn error : ncbi::CObject::ThrowNullPointerException() - Attempt to access NU
by
hophuquy0944
• 0
i have the same error, i used high performance computer, here is my code to set memory. srun --nodes=1 --ntasks=1 --cpus-per-task=24 -…
Comment: Overlapping Ranges within Granges object
by
Alex Reynolds
35k
Yes, `bedmap` will perform operations on one or two BED files.
Comment: B allele frequency (BAF)
by
aidangcruickshank
▴ 10
Apologies for resurrecting this post, but any idea what that functions "regions" paramater takes? Would it be a GRanges object? The documen…
Comment: How to handle duplicated genes in TCGA data?
by
Ngrin
• 0
Thanks @txema.heredia.The tool I am going to use only accepts gene symbols. This is the reason. So I cannot use ENS IDs.
Answer: Design for complex RNA-Seq experiment using Deseq2
by
swbarnes2
14k
This is a rather small experiment, I don't know that you can establish a meaningful baseline for each patient with a single pre sample, and…
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