From f01fb617dc5fe23db60d17c3f2c03523fb08619b Mon Sep 17 00:00:00 2001
From: Maarten de Vries <31576278+maarten-devries@users.noreply.github.com>
Date: Thu, 11 May 2023 15:34:10 -0400
Subject: [PATCH 1/5] Update requirements.txt

---
 requirements.txt | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/requirements.txt b/requirements.txt
index 0c7c0e9..13b97b9 100644
--- a/requirements.txt
+++ b/requirements.txt
@@ -10,4 +10,4 @@ tqdm==4.64.1
 seaborn==0.12.1
 matplotlib==3.6.2
 scikit-misc==0.1.4
-torch==">=1.8.0"
+torch>=1.8.0

From 525bc389c7bb766c9aa47770a4b269aa3c89fde1 Mon Sep 17 00:00:00 2001
From: Maarten de Vries <31576278+maarten-devries@users.noreply.github.com>
Date: Thu, 11 May 2023 15:40:22 -0400
Subject: [PATCH 2/5] Update README.md

change `GeneVectorTrainer` to `GeneVectorModel`
---
 README.md | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/README.md b/README.md
index a7299ed..8eab7d6 100644
--- a/README.md
+++ b/README.md
@@ -35,7 +35,7 @@ GeneVector makes use of Scanpy anndata objects and requires that the raw count d
 
 ```
 from genevector.data import GeneVectorDataset
-from genevector.model import GeneVectorTrainer
+from genevector.model import GeneVectorModel
 from genevector.embedding import GeneEmbedding, CellEmbedding
 
 import scanpy as sc

From 44a08a8666bf1f19da767a7c7b14cda8f73dfa81 Mon Sep 17 00:00:00 2001
From: Maarten de Vries <31576278+maarten-devries@users.noreply.github.com>
Date: Thu, 11 May 2023 15:49:13 -0400
Subject: [PATCH 3/5] Update README.md

---
 README.md | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/README.md b/README.md
index 8eab7d6..121b2a2 100644
--- a/README.md
+++ b/README.md
@@ -35,7 +35,7 @@ GeneVector makes use of Scanpy anndata objects and requires that the raw count d
 
 ```
 from genevector.data import GeneVectorDataset
-from genevector.model import GeneVectorModel
+from genevector.model import GeneVectorModel, GeneVector
 from genevector.embedding import GeneEmbedding, CellEmbedding
 
 import scanpy as sc

From 42796d25f76e7c43a206afdea012463ceadfe690 Mon Sep 17 00:00:00 2001
From: Maarten de Vries <31576278+maarten-devries@users.noreply.github.com>
Date: Thu, 11 May 2023 15:53:45 -0400
Subject: [PATCH 4/5] Update README.md

---
 README.md | 1 -
 1 file changed, 1 deletion(-)

diff --git a/README.md b/README.md
index 121b2a2..af539fe 100644
--- a/README.md
+++ b/README.md
@@ -50,7 +50,6 @@ After loading the expression, creating a GeneVector object will compute the mutu
 cmps = GeneVector(dataset,
                   output_file="genes.vec",
                   emb_dimension=100,
-                  threshold=1e-6,
                   device="cuda")
 cmps.train(1000, threshold=1e-6) # run for 1000 iterations or loss delta below 1e-6.
 ```

From 0c93df9687baa0d8892cc8d887f212132d9da59a Mon Sep 17 00:00:00 2001
From: Maarten de Vries <31576278+maarten-devries@users.noreply.github.com>
Date: Thu, 11 May 2023 15:57:14 -0400
Subject: [PATCH 5/5] fix typo

---
 README.md | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/README.md b/README.md
index af539fe..5a155d0 100644
--- a/README.md
+++ b/README.md
@@ -68,7 +68,7 @@ gembed = GeneEmbedding("genes.vec", dataset, vector="average")
 ```
 
 #### 1. Computing gene similarities
-A pandas dataframe can be generated using ```compute_similarities``` that includes the most similar genes and their cosine similarities for a given gene query. A barplot figure with a specified number of the most similar genes can be generated using ```plots_similarities```.
+A pandas dataframe can be generated using ```compute_similarities``` that includes the most similar genes and their cosine similarities for a given gene query. A barplot figure with a specified number of the most similar genes can be generated using ```plot_similarities```.
 
 ```
 df = gembed.compute_similarities("CD8A")