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729 results • Page
1 of 15
Sort: Rank
Rank
Views
Votes
Replies
82
votes
46
replies
8.1k
views
15 follow
Tool:
ChatGPT optimized for bioinformatics questions
gpt
updated 5 days ago by
LauferVA
4.0k • written 9 months ago by
Sasha
▴ 830
5
votes
2
replies
2.5k
views
Tool:
Coovar: Co-Occurring Variant Analyzer
snp
variant-annotation
updated 11 days ago by
GenoMax
140k • written 11.4 years ago by
Christian
★ 3.0k
1
vote
4
replies
335
views
Tool:
A c library for reading and writing sequences in fasta and fastq format.
seqio
12 days ago by
dwpeng
• 0
1
vote
0
replies
206
views
Tool:
HFKReads, an ultra-fast and efficient tool for high frequency kmer sequencing reads extraction
kmer
organelle
metagenomic
assembly
22 days ago by
Huiyang
▴ 150
0
votes
0
replies
214
views
Tool:
Microbiome Analysis: Comprehensive 16S Meta-barcoding Analysis in R with Phyloseq - On Sale Now!
R
microbiome
16S
phyloseq
analysis
17 days ago by
camillatafuro
• 0
0
votes
0
replies
138
views
Tool:
Annotating the epitope-specificity of TCRs with bioinformatics
Annotation
TCR
Epitope-specificity
4 weeks ago by
tim
• 0
10
votes
12
replies
1.6k
views
Tool:
PanDepth, an ultra-fast and efficient genomic tool for coverage calculation
bam
paf
depth
cram
coverage
4 weeks ago by
Huiyang
▴ 150
1
vote
0
replies
177
views
Tool:
gxf2bed: A high-performance GTF/GFF-to-BED converter written in Rust
convert
gff
gtf
bed
5 weeks ago by
alejandrogzi
▴ 120
3
votes
8
replies
579
views
Tool:
Generate unit-tested, ready-to-run pipelines using natural language prompting
NGS
pipeline
genomics
cloud
AI
updated 5 weeks ago by
Ram
43k • written 6 weeks ago by
Kevin
▴ 50
3
votes
0
replies
148
views
Tool:
GW: fast genome browser and variant exploration tool
genome
genomics
variant-annotation
genome-browser
visualization
6 weeks ago by
clealk
▴ 40
1
vote
0
replies
180
views
Tool:
BIRCH3.90 - BioLegato, Apple Silicon, Updates
genomics
sequence
transcriptomics
7 weeks ago by
brian.fristensky
▴ 460
0
votes
0
replies
153
views
Tool:
Get `BPCells` with Bioconductor workflow
single
cell
BPCells
8 weeks ago by
Yun
• 0
1
vote
3
replies
573
views
Tool:
retroSeeker: discovering a large set of retrotransposons in humans and any species
Mobile-element
Evolution
Retrotransposon
9 weeks ago by
lsp03yjh
▴ 860
1
vote
0
replies
214
views
Tool:
tinybio in OpenAI App Store
gpt
9 weeks ago by
Sasha
▴ 830
0
votes
0
replies
831
views
Tool:
What do you think about Tfinder? a tool to find individual motifs in DNA sequence. Help us ameliorate
Motifs
Transcription-factor
updated 12 weeks ago by
Ram
43k • written 12 weeks ago by
Naima
• 0
0
votes
2
replies
326
views
Tool:
Dot_plot_like_in_BLAST, a standalone tool for making dot plots similar to what online BLAST makes
Megablast
Blastn
dot
plot
dotplot
BLAST
updated 12 weeks ago by
Ram
43k • written 12 weeks ago by
shelkmike
★ 1.2k
1
vote
0
replies
217
views
Tool:
De Novo assembler (in C, supports MPI parallelism) available for experimenting with
de-novo
trie
olc
updated 3 months ago by
Ram
43k • written 3 months ago by
Graham
▴ 10
4
votes
0
replies
412
views
Tool:
NOEL: An extremely fast Non-Overlapping Exon Length calculator written in Rust
gene-annotation
exon-length
3 months ago by
alejandrogzi
▴ 120
9
votes
4
replies
2.2k
views
Tool:
SEDA (SEquence DAtaset builder): a desktop tool for processing FASTA files containing DNA and protein sequences
fasta
sequences
java
3 months ago by
Hugo
▴ 380
0
votes
0
replies
512
views
Tool:
deepBreaks: a machine learning tool for identifying and prioritizing genotype-phenotype associations
python
genetics
updated 4 months ago by
Ram
43k • written 4 months ago by
Mahdi
• 0
1
vote
1
reply
357
views
Tool:
Coremine Medical Introduction - connect - discover - share | explore and visualize associations
drug-target
drug
gene
updated 4 months ago by
Ram
43k • written 4 months ago by
Coremine Medical
▴ 20
0
votes
0
replies
208
views
Tool:
massSight: A tool to combine LC-MS datasets
qc
metabolomics
omics
R
lc-ms
4 months ago by
Chiraag
• 0
0
votes
0
replies
254
views
Tool:
Coremine Medical used in study to discover differentially expressed genes in multiple sclerosis
drugs
drug-targets
genes
4 months ago by
Coremine Medical
▴ 20
0
votes
0
replies
284
views
Tool:
Introducing SpectraView - a tool to transform your literature reviews!
gene
protein
drug-discovery
updated 4 months ago by
Ram
43k • written 4 months ago by
DrugDiscoveryTech
• 0
4
votes
0
replies
326
views
Tool:
MyBrain-Seq: A Pipeline for MiRNA-Seq Data Analysis in Neuropsychiatric Disorders
mybrain-seq
miRNA-seq
pipeline
neuropsychiatry
docker
5 months ago by
dannyzimm
▴ 50
12
votes
4
replies
956
views
Tool:
BBTools 39.03 released!
BBTools
BBMap
5 months ago by
Brian Bushnell
20k
2
votes
2
replies
544
views
Tool:
Python and R without installing apps
Resources
updated 6 months ago by
jena
▴ 290 • written 6 months ago by
gallardodiazmiriam
▴ 20
0
votes
0
replies
268
views
Tool:
MTMCSKAT package for GWAS with efficient resampling, parallelization
SKAT
MTMC-SKAT
updated 6 months ago by
Ram
43k • written 6 months ago by
michael.nagle
▴ 100
11
votes
2
replies
726
views
Tool:
Pipeline Generator
gpt
updated 7 months ago by
LauferVA
4.0k • written 7 months ago by
Sasha
▴ 830
13
votes
6
replies
5.0k
views
Tool:
csvtk - a cross-platform, efficient, practical and pretty CSV/TSV toolkit
CSV
Golang
TSV
7 months ago by
shenwei356
8.4k
3
votes
1
reply
685
views
Tool:
pyGenomeViz - A genome visualization python package for comparative genomics
genome
comparative-genomics
python
microbial-genomics
visualization
updated 8 weeks ago by
n.s.j.vandervelden
▴ 90 • written 7 months ago by
moshi
▴ 150
9
votes
9
replies
4.3k
views
Tool:
pyCirclize - Circular visualization in Python
visualization
circos
matplotlib
genome
python
updated 7 months ago by
shuo
• 0 • written 15 months ago by
moshi
▴ 150
0
votes
2
replies
6.6k
views
Tool:
The script to install the required packages for gene expression analysis using DESeq2 for downstream analysis and visualization
R
RNAseq
installation
DESeq2
7 months ago by
Aditya naman
• 0
1
vote
0
replies
519
views
Tool:
Create realistic VCF genomic data in just a few lines of Python code
genomic
linkage
python
vcf
tool
disequilibrium
7 months ago by
Rémy
▴ 10
1
vote
2
replies
3.5k
views
Tool:
How Study Aromatic-Aromatic Interactions And Amino-Aromatic Interactions Of Protein-Ligands Complexes In The Pdb.
pdb
updated 8 months ago by
Jiyao Wang
▴ 370 • written 10.4 years ago by
bagaruwa
• 0
3
votes
2
replies
704
views
Tool:
Launched: Genozip 15 with co-compression of BAM and FASTQ
BAM
CRAM
compression
FASTQ
updated 8 months ago by
DBScan
▴ 300 • written 8 months ago by
Divon
▴ 230
0
votes
0
replies
376
views
Tool:
tinybio added sources & chat history - (ChatGPT optimized for bioinformatics questions)
gpt
8 months ago by
Sasha
▴ 830
7
votes
4
replies
2.8k
views
Tool:
TreeView3 - An update to java TreeView
TreeView3
java
updated 7 months ago by
nach.mcnach
▴ 10 • written 5.7 years ago by
rleach
▴ 180
0
votes
0
replies
332
views
Tool:
Unleashing the Power of Custom NGS Software for Cutting-Edge Research
DNAseq
pipeline
bisulfiteSeq
RNAseq
updated 9 months ago by
rpolicastro
13k • written 9 months ago by
David Langenberger
11k
5
votes
3
replies
801
views
Tool:
Experiment Generator
gpt
updated 9 months ago by
LauferVA
4.0k • written 9 months ago by
Sasha
▴ 830
0
votes
0
replies
464
views
Tool:
Easy API For Running Bioinformatics Jobs Via Python In The Cloud
api
execution
9 months ago by
Sasha
▴ 830
0
votes
0
replies
428
views
Tool:
Single-cell RNA-seq data analysis tool Cellenics®
single-cell
RNA-seq
scRNA-seq
updated 10 months ago by
Ram
43k • written 10 months ago by
Anastasija
• 0
0
votes
1
reply
924
views
Tool:
web app for user-friendly analysis of 16S rRNA gene meta-barcoding NGS data - bacterial microbiome
qiime2
16s
microbiome
ngs
updated 10 months ago by
Ram
43k • written 10 months ago by
camillatafuro
• 0
1
vote
2
replies
808
views
Tool:
Tinybio Slackbot - a large language model slackbot for bioinformatics
qa
10 months ago by
Sasha
▴ 830
0
votes
0
replies
420
views
Tool:
shinyCircos-V2.0: leveraging the creation of Circos plot with enhanced usability and advanced features
shinyCircos
visualization
Circular
Circos
genome
10 months ago by
Andrewoods
▴ 110
361
votes
81
replies
143k
views
34 follow
Tool:
Gnu Parallel - Parallelize Serial Command Line Programs Without Changing Them
parallel
next-gen
ngs
11 months ago by
ole.tange
★ 4.4k
0
votes
0
replies
3.2k
views
Tool:
euka: Robust detection of eukaryotic taxa from modern and ancient environmental DNA using pangenomic reference graphs.
pangenomics
vg
sedaDNA
graph
environmental-DNA
updated 11 months ago by
Ram
43k • written 11 months ago by
Nicola
▴ 10
0
votes
1
reply
404
views
Tool:
TRcaller : a novel Tool for SSR /STR/TR genotyping from NGS data for short and long reads
SSR
NGS
genotype
STR
updated 11 months ago by
Ram
43k • written 11 months ago by
Xuewen
• 0
46
votes
9
replies
42k
views
7 follow
Tool:
Tools to merge overlapping paired-end reads
ngs
Assembly
fastq
updated 11 months ago by
Charles-Alexandre Roy
▴ 40 • written 7.3 years ago by
Abdul Rafay Khan
★ 1.2k
4
votes
0
replies
788
views
Tool:
PyComplexHeatmap: a Python package to visualize multimodal genomics data
visualization
Python
ComplexHeatmap
PyComplexHeatmap
updated 11 months ago by
Ram
43k • written 11 months ago by
Wubin
▴ 40
729 results • Page
1 of 15
Recent Votes
Answer: Differential express genes in imbalance groups
Answer: Differential express genes in imbalance groups
Comment: Differential express genes in imbalance groups
Answer: Differential express genes in imbalance groups
Comment: Differential expression at pathway level
A: Difference between heatmap using Euclidian distance and Poisson distance
A: Difference between heatmap using Euclidian distance and Poisson distance
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aUser
▴ 30
Teacher
to
Gordon Smyth
★ 6.9k
Popular Question
to
H.Hasani
▴ 990
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kcarey
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▴ 150
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Duarte Molha
▴ 240
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Zhenyu Zhang
★ 1.1k
Recent Replies
Answer: Downloading epigenetic and mutation data of specific TCGA BRCA samples
by
aUser
▴ 30
Hi, you might have solve the problem, but for the future reference, I am writing this. The nomenclature of TCGA data set is explained here:…
Comment: error in wigToBigWig while converting mappability to bedgraph
by
Dora
▴ 10
Thank you so much for your reply! here is what I have after entering the command variableStep#chrom=NT_173277.1 Cavia porcellus strain…
Comment: Differential express genes in imbalance groups
by
Chris
▴ 260
Wow, the author of the tool reply. Thank you so much!
Comment: t-test in two groups, multiple rows
by
sooni
▴ 20
It was my mistake. I converted the dataframe to matrix. It works! Thank you!
Comment: Differential express genes in imbalance groups
by
Gordon Smyth
★ 6.9k
I do mean the quality of each sample (as measured by residual variability in the linear model, in other words by consistency with other sam…
Comment: Differential express genes in imbalance groups
by
Chris Dean
▴ 390
That sounds super interesting. I have never heard of this approach before. When you say 'sample quality weights' are you referring to dif…
Answer: Beagle Phasing and Imputation
by
LChart
3.8k
Not doable with older versions of beagle. I seem to recall that it used to be recommended to re-code the sex chromosomes of males in the re…
Answer: Differential express genes in imbalance groups
by
Gordon Smyth
★ 6.9k
Imbalanced group sizes are no problem. Just analyse the data as it is. No need to throw data away! For a human study with a large number o…
Comment: Trim Galore: Automatic detection of adapters
by
Daniel
▴ 30
Got it, this clears things up. Thank you!
Answer: basal gene expression level
by
LChart
3.8k
I haven't seen any reliable way to estimate absolute RNA concentrations from sequencing data. Methods have been developed using [housekeepi…
Answer: Seurat 5 integration
by
jared.andrews07
★ 16k
You are still free to change whichever parameters you want for whichever method you're using. See `?IntegrateLayers` and whichever method y…
Answer: scRNAseq normalization
by
ATpoint
81k
It's perfectly fine to use log-transformation. The advantages of these more complicated methods usually depend on context and also on the w…
Answer: scRNAseq normalization
by
dsull
★ 5.6k
No, your log-transform might indeed be ok (or even better) for your analysis of interest. See https://www.nature.com/articles/s41592-023…
Answer: Transcription Start Site
by
el24
▴ 40
Here is a simple pythonic way to use biomart: import pybiomart as pbm dataset = pbm.Dataset(name='hsapiens_gene_ensembl', host="h…
Comment: data background noise
by
marco.barr
▴ 30
Thank you very much for your response. I've been calling it background noise, but perhaps we're saying the same thing. I mean, I really wan…
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